uniQure N.V. 10-K

Item 9A. Controls and Procedures . ​ Evaluation of Disclosure Controls and Procedures ​ Our management, with the participation of our chief executive officer (“CEO”, our principal executive officer) and chief financial officer (“CFO”, our principal financial officer), evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act) as of December 31, 2025. Based on such evaluation, our CEO and CFO have concluded that as of December 31, 2025, our disclosure controls and procedures were effective. 114 ​ Table of Contents Management’s Annual Report on Internal Control Over Financial Reporting ​ Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act. This rule defines internal control over financial reporting as a process designed by, or under the supervision of, a company’s chief executive officer and chief financial officer and effected by our board of directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles and includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of our assets that could have a material effect on the financial statements. ​ We assessed the effectiveness of our internal control over financial reporting as of December 31, 2025. This assessment was performed under the direction and supervision of our CEO and CFO and based on criteria established in Internal Control - Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO”). Our management’s assessment of the effectiveness of our internal control over financial reporting included testing and evaluating the design and operating effectiveness of our internal controls. In our management’s opinion, we have maintained effective internal control over financial reporting as of December 31, 2025, based on criteria established in the COSO 2013 framework. ​ Our independent registered public accounting firm, which has audited the consolidated financial statements included in this Annual Report on Form 10-K, has also issued an audit report on the effectiveness of our internal control over financial reporting as of December 31, 2025. Their report is filed within this Annual Report on Form 10-K. ​ Inherent Limitations of Internal Controls Our management, including our CEO and CFO, does not expect that our disclosure controls and procedures or our internal controls will prevent all errors and all fraud. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the control system are met. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within the Company have been detected. These inherent limitations include the realities that judgments in decision-making can be faulty, and that breakdowns can occur because of a simple error or mistake. Additionally, controls can be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the control. The design of any system of controls also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Over time, controls may become inadequate because of changes in conditions, or the degree of compliance with the policies or procedures may deteriorate. Projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements due to error or fraud. ​ Changes in internal control over financial reporting During the fourth quarter of 2025, there were no changes in our internal control over financial reporting (as defined in Rule 13a-15(f) under the Exchange Act) that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. ​ ​ ​ ​ 115 ​ Table of Contents Item 9B. Other Information Trading Arrangements During the three months ended December 31, 2025, the following adopted a “ Rule 10b5-1 trading arrangement ” (as defined in Item 408(a) of Regulation S-K) that is intended to satisfy the affirmative defense of Rule 10b5-1(c) under the Exchange Act and our policies on insider trading: ​ ​ ​ ​ ​ Name & Title Date Adopted (1) Aggregate Number of Ordinary Shares to be Purchased or Sold Pursuant to Trading Arrangement Expiration Date (2) Matthew Kapusta , Chief Executive Officer October 5, 2025 332,576 November 1, 2026 Jeannette Potts , Chief Legal Officer October 2, 2025 45,730 December 31, 2026 Jeremy Springhorn , Non-executive Director October 3, 2025 10,000 December 30, 2027 ​ (1) Date of adoption of this Rule 10b5-1 trading arrangement is in accordance with applicable SEC rules and regulations. The first trade pursuant to this Rule 10b5-1 trading arrangement will be, in accordance with applicable SEC rules and regulations, on a date after the date of adoption of the Rule 10b5-1 trading arrangement, to the extent triggered under its terms. ​ (2) The Rule 10b5-1 trading arrangement is scheduled to expire on the date listed in the table, subject to earlier termination upon the sale of all shares subject to the Rule 10b5-1 trading arrangement, or as otherwise provided in the Rule 10b5-1 trading arrangement. ​ Other than those disclosed above, none of our directors or officers adopted, modified, or terminated a “Rule 10b5-1 trading arrangement” or “ non-Rule 10b5-1 trading arrangement ,” in each case as defined in Item 408 of Regulation S-K, during the three months ended December 31, 2025. ​ Item 9C. Disclosure Regarding Foreign Jurisdictions that Prevent Inspections ​ None. ​ Part III ​ Item 10. Directors, Executive Officers and Corporate Governance We maintain an insider trading policy governing the purchase, sale and/or other dispositions of our securities by our directors, officers, employees, consultants and contractors, as well as the Company itself. We believe that the insider trading policy is reasonably designed to promote compliance with insider trading laws, rules and regulations, as well as the applicable laws and regulations of the Nasdaq listing standards. A copy of our insider trading policy is filed as Exhibit 19.1 to this Annual Report on Form 10-K. The remaining information required by Item 10 is incorporated by reference from our Proxy Statement for our 2026 annual meeting of shareholders, which we will file within 120 days of December 31, 2025, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 11. Executive Compensation ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2026 annual meeting of shareholders, which we will file within 120 days of December 31, 2025, or will be included in an amendment to this Annual Report on Form 10-K. ​ ​ 116 ​ Table of Contents Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2026 annual meeting of shareholders, which we will file within 120 days of December 31, 2025, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 13. Certain Relationships and Related Transactions, and Director Independence The information required by this item is incorporated by reference from our Proxy Statement for our 2026 annual meeting of shareholders, which we will file within 120 days of December 31, 2025, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 14. Principal Accounting Fees and Services The information required by this item is incorporated by reference from our Proxy Statement for our 2026 annual meeting of shareholders, which we will file within 120 days of December 31, 2025, or will be included in an amendment to this Annual Report on Form 10-K. ​ ​ 117 ​ Table of Contents Part IV ​ Item 15. Exhibits, Financial Statements Schedules ​ Exhibits, Financial Statements Schedules ​ (a) Financial Statements . The following consolidated financial statements of uniQure N.V. are filed as part of this report: ​ ​ Page Report of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 120 Consolidated Balance Sheets as of December 31, 2025 and 2024 122 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2025, 2024 and 2023 123 Consolidated Statements of Shareholders’ Equity / (Deficit) for the Years Ended December 31, 2025, 2024 and 2023 124 Consolidated Statements of Cash Flows for the Years Ended December 31, 2025, 2024 and 2023 125 Notes to Consolidated Financial Statements for the Years Ended December 31, 2025, 2024 and 2023 126 ​ (b) Financial Statements Schedules . Financial Statement Schedules have been omitted because of the absence of conditions under which they are required or because the required information, where material, is shown in the financial statements or notes. ​ (c) Other Exhibits . The Exhibit Index immediately preceding the signature page of this Annual Report on Form 10-K is incorporated herein by reference. ​ Item 16. Form 10-K Summary ​ Not applicable. ​ ​ 118 ​ Table of Contents ​ INDEX TO CONSOLIDATED FINANCIAL STATEMENTS FOR THE YEARS ENDED DECEMBER 31, 2025, 2024 AND 2023 ​ ​ ​ Page Report of Independent Registered Public Accounting Firm - KPMG Accountants N.V., Amstelveen, The Netherlands (PCAOB ID 1012 ) 120 Consolidated Balance Sheets as of December 31, 2025 and 2024 122 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2025, 2024 and 2023 123 Consolidated Statements of Shareholders’ Equity / (Deficit) for the Years Ended December 31, 2025, 2024 and 2023 124 Consolidated Statements of Cash Flows for the Years Ended December 31, 2025, 2024 and 2023 125 Notes to Consolidated Financial Statements 126 ​ ​ 119 ​ Table of Contents Report of Independent Registered Public Accounting Firm ​ To the Shareholders and Board of Directors uniQure N.V.: ​ Opinions on the Consolidated Financial Statements and Internal Control Over Financial Reporting We have audited the accompanying consolidated balance sheets of uniQure N.V. and subsidiaries (‘the Company’) as of December 31, 2025 and 2024, the related consolidated statements of operations and comprehensive loss, shareholders’ equity / (deficit), and cash flows for each of the years in the three-year period ended December 31, 2025, and the related notes (collectively, the consolidated financial statements). We also have audited the Company’s internal control over financial reporting as of December 31, 2025, based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of the Company as of December 31, 2025 and 2024, and the results of its operations and its cash flows for each of the years in the three-year period ended December 31, 2025, in conformity with U.S. generally accepted accounting principles. Also in our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2025 based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. Basis for Opinions The Company’s management is responsible for these consolidated financial statements, for maintaining effective internal control over financial reporting, and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Management’s Annual Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the Company’s consolidated financial statements and an opinion on the Company’s internal control over financial reporting based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud, and whether effective internal control over financial reporting was maintained in all material respects. Our audits of the consolidated financial statements included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the consolidated financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements. Our audit of internal control over financial reporting included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on the assessed risk. Our audits also included performing such other procedures as we considered necessary in the circumstances. We believe that our audits provide a reasonable basis for our opinions. 120 ​ Table of Contents Definition and Limitations of Internal Control Over Financial Reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate Critical Audit Matters Critical audit matters are matters arising from the current period audit of the consolidated financial statements that were communicated or required to be communicated to the audit committee and that: (1) relate to accounts or disclosures that are material to the consolidated financial statements and (2) involved our especially challenging, subjective, or complex judgments. We determined that there are no critical audit matters. ​ /s/ KPMG Accountants N.V. ​ We have served as the Company’s auditor since 2019. Amstelveen, the Netherlands March 2, 2026 ​ ​ 121 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 80,240 ​ $ 158,930 Current investment securities ​ ​ 542,301 ​ ​ 208,591 Accounts receivable ​ ​ 5,863 ​ ​ 5,881 Prepaid expenses ​ ​ 20,506 ​ ​ 9,281 Other current assets and receivables ​ ​ 7,076 ​ ​ 7,606 Total current assets ​ ​ 655,986 ​ ​ 390,289 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net ​ ​ 13,800 ​ ​ 20,424 Other investments ​ ​ 30,237 ​ ​ 27,464 Operating lease right-of-use assets ​ ​ 12,525 ​ ​ 13,647 Intangible assets, net ​ ​ 72,790 ​ ​ 71,043 Goodwill ​ ​ 25,355 ​ ​ 22,414 Deferred tax assets, net ​ ​ 8,654 ​ ​ 9,856 Other non-current assets ​ ​ 5,561 ​ ​ 1,399 Total non-current assets ​ ​ 168,922 ​ ​ 166,247 Total assets ​ $ 824,908 ​ $ 556,536 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 5,170 ​ $ 7,227 Accrued expenses and other current liabilities ​ ​ 41,292 ​ ​ 29,225 Liability related to pre-funded warrants ​ ​ 12,595 ​ ​ — Current portion of operating lease liabilities ​ ​ 3,862 ​ ​ 3,601 Total current liabilities ​ ​ 62,919 ​ ​ 40,053 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 49,699 ​ ​ 51,324 Liability from royalty financing agreement ​ ​ 473,199 ​ ​ 434,930 Operating lease liabilities, net of current portion ​ ​ 9,832 ​ ​ 11,136 Contingent consideration ​ ​ 18,736 ​ ​ 10,860 Deferred tax liability, net ​ ​ 7,967 ​ ​ 7,043 Other non-current liabilities, net of current portion ​ ​ 3,655 ​ ​ 7,942 Total non-current liabilities ​ ​ 563,088 ​ ​ 523,235 Total liabilities ​ ​ 626,007 ​ ​ 563,288 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity / (deficit) ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of December 31, 2025 and December 31, 2024 and 62,336,717 and 48,988,087 ordinary shares issued and outstanding as of December 31, 2025 and December 31, 2024, respectively ​ ​ 3,688 ​ ​ 2,945 Additional paid-in-capital ​ ​ 1,582,371 ​ ​ 1,173,068 Accumulated other comprehensive loss ​ ​ ( 58,222 ) ​ ​ ( 52,800 ) Accumulated deficit ​ ​ ( 1,328,936 ) ​ ​ ( 1,129,965 ) Total shareholders' equity / (deficit) ​ ​ 198,901 ​ ​ ( 6,752 ) Total liabilities and shareholders' equity / (deficit) ​ $ 824,908 ​ $ 556,536 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 122 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ 2023 ​ ​ (in thousands, except share and per share amounts) License revenues ​ $ 15,934 ​ $ 10,133 ​ $ 2,758 Contract manufacturing revenues ​ ​ — ​ ​ 6,114 ​ ​ 10,835 Collaboration revenues ​ ​ 164 ​ ​ 10,872 ​ ​ 2,250 Total revenues ​ ​ 16,098 ​ ​ 27,119 ​ ​ 15,843 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 1,686 ) ​ ​ ( 1,267 ) ​ ​ ( 65 ) Cost of contract manufacturing revenues ​ ​ — ​ ​ ( 17,060 ) ​ ​ ( 13,563 ) Research and development expenses ​ ​ ( 140,673 ) ​ ​ ( 143,782 ) ​ ​ ( 214,864 ) Selling, general and administrative expenses ​ ​ ( 65,456 ) ​ ​ ( 52,657 ) ​ ​ ( 74,591 ) Total operating expenses ​ ​ ( 207,815 ) ​ ​ ( 214,766 ) ​ ​ ( 303,083 ) Other income ​ ​ 14,410 ​ ​ 7,926 ​ ​ 6,059 Other expense ​ ​ ( 8,042 ) ​ ​ ( 4,573 ) ​ ​ ( 1,690 ) Loss from operations ​ ​ ( 185,349 ) ​ ​ ( 184,294 ) ​ ​ ( 282,871 ) Interest income ​ ​ 16,967 ​ ​ 21,415 ​ ​ 19,562 Interest expense ​ ​ ( 61,994 ) ​ ​ ( 63,741 ) ​ ​ ( 41,557 ) Foreign currency gains / (losses), net ​ ​ 26,131 ​ ​ ( 10,507 ) ​ ​ ( 1,691 ) Other non-operating gains, net ​ ​ 10,905 ​ ​ — ​ ​ — Loss before income tax expense ​ $ ( 193,340 ) ​ $ ( 237,127 ) ​ $ ( 306,557 ) Income tax expense ​ ​ ( 5,631 ) ​ ​ ( 2,429 ) ​ ​ ( 1,921 ) Net loss ​ $ ( 198,971 ) ​ $ ( 239,556 ) ​ $ ( 308,478 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation (losses) / gains, net ​ ​ ( 6,193 ) ​ ​ 426 ​ ​ 6,874 Defined benefit pension gain / (loss), net of taxes ​ ​ 771 ​ ​ 327 ​ ​ ( 2,136 ) Total comprehensive loss ​ $ ( 204,393 ) ​ $ ( 238,803 ) ​ $ ( 303,740 ) Loss per ordinary share - basic and diluted ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 3.46 ) ​ $ ( 4.92 ) ​ $ ( 6.47 ) Weighted average shares - basic and diluted ​ ​ 57,502,068 ​ ​ 48,649,129 ​ ​ 47,670,986 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 123 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY / (DEFICIT) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ ​ ​ ​ No. of shares ​ ​ ​ Amount ​ ​ ​ capital ​ ​ ​ loss ​ ​ ​ deficit ​ ​ ​ equity / (deficit) ​ ​ (in thousands, except share and per share amounts) Balance at December 31, 2022 ​ 46,968,032 ​ $ 2,838 ​ $ 1,113,393 ​ $ ( 58,291 ) ​ $ ( 581,931 ) ​ $ 476,009 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 308,478 ) ​ ​ ( 308,478 ) Other comprehensive income, net ​ — ​ ​ — ​ ​ — ​ ​ 4,738 ​ ​ — ​ ​ 4,738 Exercises of share options ​ 14,070 ​ ​ 1 ​ ​ 129 ​ ​ — ​ ​ — ​ ​ 130 Restricted and performance share units distributed during the period ​ 832,530 ​ ​ 43 ​ ​ ( 43 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 35,093 ​ ​ — ​ ​ — ​ ​ 35,093 Issuance of ordinary shares relating to employee stock purchase plan ​ 19,198 ​ ​ 1 ​ ​ 177 ​ ​ — ​ ​ — ​ ​ 178 Balance at December 31, 2023 ​ 47,833,830 ​ $ 2,883 ​ $ 1,148,749 ​ $ ( 53,553 ) ​ $ ( 890,409 ) ​ $ 207,670 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 239,556 ) ​ ​ ( 239,556 ) Other comprehensive income, net ​ — ​ ​ — ​ ​ — ​ ​ 753 ​ ​ — ​ ​ 753 Exercises of share options ​ 169,898 ​ ​ 9 ​ ​ 2,065 ​ ​ — ​ ​ — ​ ​ 2,074 Restricted share units distributed during the period ​ 974,209 ​ ​ 52 ​ ​ ( 52 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 22,258 ​ ​ — ​ ​ — ​ ​ 22,258 Issuance of ordinary shares relating to employee stock purchase plan ​ 10,150 ​ ​ 1 ​ ​ 48 ​ ​ — ​ ​ — ​ ​ 49 Balance at December 31, 2024 ​ 48,988,087 ​ $ 2,945 ​ $ 1,173,068 ​ $ ( 52,800 ) ​ $ ( 1,129,965 ) ​ $ ( 6,752 ) Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 198,971 ) ​ ​ ( 198,971 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 5,422 ) ​ ​ — ​ ​ ( 5,422 ) Follow-on public offerings ​ 11,810,370 ​ ​ 655 ​ ​ 380,082 ​ ​ — ​ ​ — ​ ​ 380,737 Tax benefit related to historical share issuance costs ​ — ​ ​ — ​ ​ 468 ​ ​ ​ ​ ​ ​ ​ ​ 468 Exercises of share options ​ 694,879 ​ ​ 42 ​ ​ 11,120 ​ ​ — ​ ​ — ​ ​ 11,162 Restricted and performance share units distributed during the period ​ 843,381 ​ ​ 46 ​ ​ ( 46 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 17,679 ​ ​ — ​ ​ — ​ ​ 17,679 Balance at December 31, 2025 ​ 62,336,717 ​ $ 3,688 ​ $ 1,582,371 ​ $ ( 58,222 ) ​ $ ( 1,328,936 ) ​ $ 198,901 ​ The accompanying notes are an integral part of these consolidated financial statements ​ 124 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 198,971 ) ​ $ ( 239,556 ) ​ $ ( 308,478 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation and amortization ​ ​ 14,759 ​ ​ 12,641 ​ ​ 11,900 Amortization of discount on investment securities ​ ​ ( 10,463 ) ​ ​ ( 10,901 ) ​ ​ ( 10,917 ) Share-based compensation expense ​ ​ 17,679 ​ ​ 22,258 ​ ​ 35,093 Royalty financing agreement interest expense, net of interest paid ​ ​ 38,841 ​ ​ 44,203 ​ ​ 25,616 Deferred tax expense ​ ​ 1,588 ​ ​ 2,429 ​ ​ 1,921 Changes in fair value of contingent consideration ​ ​ 6,247 ​ ​ ( 1,817 ) ​ ​ 15,895 Changes in fair value of liability related to pre-funded warrants ​ ​ ( 12,405 ) ​ ​ — ​ ​ — Unrealized foreign exchange (gains) / losses, net ​ ​ ( 23,019 ) ​ ​ 15,415 ​ ​ ( 2,206 ) Other items, net ​ ​ ( 5,429 ) ​ ​ ( 3,848 ) ​ ​ 4,721 Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ ( 8,597 ) ​ ​ ( 2,243 ) ​ ​ ( 1,323 ) Accounts payable ​ ​ ( 2,667 ) ​ ​ 1,520 ​ ​ ( 4,169 ) Accrued expenses, other liabilities, and operating leases ​ ​ 4,474 ​ ​ ( 5,642 ) ​ ​ ( 5,328 ) Contingent consideration milestone payments ​ ​ — ​ ​ ( 19,608 ) ​ ​ ( 1,914 ) Inventories ​ ​ — ​ ​ 2,421 ​ ​ ( 6,740 ) Contract asset related to CSL Behring milestone payments ​ ​ — ​ ​ — ​ ​ 100,000 Net cash used in operating activities ​ ​ ( 177,963 ) ​ ​ ( 182,728 ) ​ ​ ( 145,929 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Proceeds on maturity of debt securities ​ ​ 337,195 ​ ​ 534,498 ​ ​ 167,907 Investment in debt securities ​ ​ ( 658,375 ) ​ ​ ( 359,841 ) ​ ​ ( 366,439 ) Divestment of commercial manufacturing facility ​ ​ — ​ ​ ( 8,321 ) ​ ​ — Purchases of property, plant, and equipment ​ ​ ( 439 ) ​ ​ ( 3,368 ) ​ ​ ( 7,154 ) Net cash (used in) / generated from investing activities ​ ​ ( 321,619 ) ​ ​ 162,968 ​ ​ ( 205,686 ) Cash flows from financing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Proceeds from follow-on public offerings of ordinary shares, net of issuance costs ​ ​ 380,737 ​ ​ — ​ ​ — Proceeds from issuance of pre-funded warrants, net of issuance costs ​ ​ 23,499 ​ ​ — ​ ​ — Proceeds from issuance of ordinary shares related to employee stock options and purchase plans ​ ​ 11,162 ​ ​ 2,123 ​ ​ 308 Repayment of long-term debt ​ ​ — ​ ​ ( 53,050 ) ​ ​ — Contingent consideration milestone payments ​ ​ — ​ ​ ( 8,559 ) ​ ​ ( 7,649 ) Proceeds from royalty financing agreement, net of issuance costs ​ ​ — ​ ​ — ​ ​ 370,062 Net cash generated from / (used in) financing activities ​ ​ 415,398 ​ ​ ( 59,486 ) ​ ​ 362,721 Currency effect on cash, cash equivalents and restricted cash ​ ​ 5,657 ​ ​ ( 4,969 ) ​ ​ 2,265 Net (decrease) / increase in cash, cash equivalents and restricted cash ​ ​ ( 78,527 ) ​ ​ ( 84,215 ) ​ ​ 13,371 Cash, cash equivalents and restricted cash at the beginning of period ​ ​ 160,329 ​ ​ 244,544 ​ ​ 231,173 Cash, cash equivalents and restricted cash at the end of period ​ $ 81,802 ​ $ 160,329 ​ $ 244,544 Cash and cash equivalents ​ $ 80,240 ​ $ 158,930 ​ $ 241,360 Restricted cash related to leasehold and other deposits ​ ​ 1,562 ​ ​ 1,399 ​ ​ 3,184 Total cash, cash equivalents and restricted cash ​ $ 81,802 ​ $ 160,329 ​ $ 244,544 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 25,069 ) ​ $ ( 20,567 ) ​ $ ( 16,878 ) Non-cash decrease in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ ( 99 ) ​ $ ( 672 ) ​ $ ( 513 ) ​ ​ The accompanying notes are an integral part of these consolidated financial statements. ​ ​ 125 ​ Table of Contents uniQure N.V. ​ NOTES TO CONSOLIDATED FINANCIAL STATEMENTS ​ 1. Corporate information ​ uniQure B.V. (the “Company”) was incorporated on January 9, 2012 as a private company with limited liability ( besloten vennootschap met beperkte aansprakelijkheid ) under the laws of the Netherlands. The Company is a leader in the field of gene therapy and seeks to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company’s business was founded in 1998 and was initially operated through its predecessor company, Amsterdam Molecular Therapeutics Holding N.V (“AMT”). In 2012, AMT undertook a corporate reorganization, pursuant to which uniQure B.V. acquired the entire business and assets of AMT and completed a share-for-share exchange with the shareholders of AMT. Effective February 10, 2014, in connection with its initial public offering, the Company converted into a public company with limited liability ( naamloze vennootschap ) and changed its legal name from uniQure B.V. to uniQure N.V. ​ The Company is registered in the trade register of the Dutch Chamber of Commerce ( Kamer van Koophandel ) in Amsterdam, the Netherlands under number 54385229. The Company’s headquarters are in Amsterdam, the Netherlands, and its registered office is located at Paasheuvelweg 25, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000. The Company’s website address is www.uniqure.com. ​ The Company’s ordinary shares are listed on the Nasdaq Global Select Market and trade under the symbol “QURE”. ​ 2. Summary of significant accounting policies ​ 2.1 Basis of preparation ​ The Company prepared its consolidated financial statements in compliance with generally accepted accounting principles in the United States (“U.S. GAAP”). Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”). ​ The consolidated financial statements have been prepared under the historical cost convention, except for financial instruments, contingent consideration and the liability related to pre-funded warrants, which are recorded at fair value within the Company’s Consolidated Statements of Operations and Comprehensive Loss. ​ The consolidated financial statements are presented in United States (“U.S.”) dollars ($), except where otherwise indicated. Transactions denominated in currencies other than U.S. dollars are presented in the transaction currency with the U.S. dollar amount included in parenthesis, converted at the foreign exchange rate as of the transaction date. ​ The consolidated financial statements presented have been prepared on a going concern basis based on the Company’s cash and cash equivalents as of December 31, 2025 and the Company’s budgeted cash flows for the twelve months following the issuance date. ​ 2.2 Use of estimates ​ The preparation of consolidated financial statements, in conformity with U.S. GAAP and Securities and Exchange Commission (“SEC”) rules and regulations, requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent assets and liabilities at of the date of the consolidated financial statements and reported amounts of revenues and expenses during the reporting period. Estimates and assumptions are primarily made in relation to contingent consideration related to the July 2021 acquisition of uniQure France SAS (the “uniQure France Acquisition”). If actual results differ from the Company’s estimates, or to the extent these estimates are adjusted in future periods, the Company’s results of operations could either benefit from, or be adversely affected by, any such change in estimate. ​ 126 ​ Table of Contents 2.3 Accounting policies ​ The principal accounting policies applied in the preparation of these consolidated financial statements are set out below. These policies have been consistently applied to all years presented, unless otherwise stated. ​ 2.3.1 Consolidation ​ The consolidated financial statements comprise the financial statements of the Company and its subsidiaries. Subsidiaries are all entities over which the Company has a controlling financial interest either through variable interest or through voting interest. Currently, the Company is not involved with variable interest entities. ​ Intercompany transactions, balances, income, and expenses on transactions between uniQure entities are eliminated upon consolidation. Profits and losses resulting from intercompany transactions that are recognized in assets are also eliminated. Accounting policies of subsidiaries have been changed where necessary to ensure consistency with the policies adopted by the Company. ​ 2.3.2 Current versus non-current classification ​ The Company presents assets and liabilities in the consolidated balance sheets based on current and non-current classification. ​ The term current assets is used to designate cash and other assets, or resources commonly identified as those that are reasonably expected to be realized in cash or sold or consumed during the normal operating cycle of the business. The Company’s normal operating cycle is twelve months . All other assets are classified as non-current. ​ The term current liabilities is used principally to designate obligations whose liquidation is reasonably expected to require the use of existing resources properly classifiable as current assets, the creation of other current liabilities, or with respect to the liability in relation to pre-funded warrants, the Company’s ordinary shares. Current liabilities are expected to be settled in the normal operating cycle. The pre-funded warrants are exercisable at the option of the holder and may be settled at any time. The Company classifies all other liabilities as non-current. ​ Deferred tax assets and liabilities are classified as non-current assets and liabilities, if any. ​ 2.3.3 Foreign currency translation ​ The functional currency of the Company and each of its entities (except for uniQure Inc. and uniQure Switzerland GmbH (“uniQure Switzerland”), formerly Corlieve Therapeutics AG, is the euro (€, or EUR). This represents the currency of the primary economic environment in which the entities operate. The functional currency of uniQure Inc. is the U.S. dollar ($) and the functional currency of uniQure Switzerland is the Swiss franc (CHF). The consolidated financial statements are presented in U.S. dollars. ​ Foreign currency transactions are measured and recorded in the functional currency using the exchange rates prevailing at the dates of the transactions. Foreign exchange gains and losses resulting from the settlement of such transactions and from the remeasurement of monetary assets and liabilities denominated in foreign currencies at exchange rates prevailing at the balance sheet date are recognized within the Company’s Consolidated Statements of Operations and Comprehensive Loss. ​ Upon consolidation, the assets and liabilities of foreign operations are translated into the functional currency of the shareholding entity at the exchange rates prevailing at the balance sheet date; items of income and expense are translated at monthly average exchange rates. The consolidated assets and liabilities are translated from uniQure N.V.’s functional currency, the euro, into the reporting currency, the U.S. dollar, at the exchange rates prevailing at the balance sheet date; items of income and expense are translated at monthly average exchange rates. Issued capital and additional paid-in capital are translated at historical rates with differences to the balance sheet date rate recorded as translation adjustments within Other comprehensive loss. The exchange differences arising on translation for consolidation are recognized within Accumulated other comprehensive loss. On disposal of a foreign operation, the component of Other comprehensive loss relating to that foreign operation, is recognized within the Company’s Consolidated Statements of Operations and Comprehensive Loss. 127 ​ Table of Contents 2.3.4 Fair value measurement ​ The Company measures certain assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ASC 820 , Fair Value Measurements and Disclosures requires disclosure of methodologies used in determining the reported fair values and establishes a hierarchy of inputs used when available. The three levels of the fair value hierarchy are described below: ​ ● Level 1 - Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company can access at the measurement date. ​ ● Level 2 - Valuations based on quoted prices for similar assets or liabilities in markets that are not active or models for which the inputs are observable, either directly or indirectly. ​ ● Level 3 - Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and are unobservable. ​ To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized as Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. ​ Items measured at fair value on a recurring basis include financial instruments, contingent consideration and the liability related to pre-funded warrants (Note 6, “ Fair value measurement ”). The carrying amount of cash and cash equivalents, accounts receivable from our licensing and collaboration partner, other assets, accounts payable, accrued expenses and other current liabilities reflected in the Consolidated Balance Sheets approximate their fair values due to their short-term maturities. ​ 2.3.5 Contingent consideration ​ Each reporting period, the Company revalues the contingent consideration obligations associated with the uniQure France Acquisition to their fair value, and records the changes in the fair value within research and development expenses. Changes in contingent consideration obligations result from changes in assumptions regarding the probabilities of achieving the relevant milestones, the estimated timing of achieving such milestones, and the interest rate to discount the milestone payments. The probability-adjusted payments are discounted to present value using a discount rate representing the Company’s credit risk. This discount rate is determined using the effective interest rate of the Company’s existing debt facility, adjusted for differences in maturity dates based on market data on effective yields for U.S. bonds with a CCC credit rating. ​ Payments of portions of contingent consideration initially recorded as of the July 2021 date of the uniQure France Acquisition are recorded as cash flows from financing activities, and payments, or the portion of the milestone payments representing changes in the fair value of contingent consideration subsequent to the initial recognition, are recorded as cash flows from operating activities. ​ Refer to Note 6 “ Fair value measurement ” for further information. ​ ​ 128 ​ Table of Contents 2.3.6 Liability related to pre-funded warrants ​ As part of the Company’s September 2025 follow-on public offering, the Company issued pre-funded warrants (the “Pre-Funded Warrants”), denominated in U.S. dollars. As the Pre-Funded Warrants are not denominated in the Company’s functional currency, they are not indexed to the Company’s ordinary shares in accordance with ASC 815-40, Derivatives and Hedging, Contracts in Entity’s Own Equity . The obligation to issue ordinary shares at an offering price of $ 47.50 per ordinary share, less a $ 0.0001 per ordinary share exercise price, is classified as a liability. The liability related to pre-funded warrants is accounted for at fair value in accordance with ASC 820, Fair Value Measurement . Changes in the fair value of the liability related to pre-funded warrants are recognized within Other non-operating items, net in the Company’s Consolidated Statements of Operations and Comprehensive Loss. The liability related to pre-funded warrants is classified as current due to the Pre-Funded Warrant holder’s right to exercise at any time. The Company made an accounting policy election to exclude the Pre-Funded Warrants from the denominator in the computation of basic net loss per ordinary share, as such instruments are not considered to be outstanding ordinary shares. ​ Refer to Note 6 “ Fair value measurement ” for further information. ​ 2.3.7 Divestiture of commercial manufacturing activities ​ On June 29, 2024, affiliates of the Company entered into an Asset Purchase Agreement (“APA”) with Genezen Holdings Inc. and its affiliate Genezen MA, Inc. (together “Genezen”). Pursuant to the APA, the Company sold its commercial manufacturing activities located in Lexington, MA (the “Lexington Transaction”) to Genezen. The Lexington Transaction closed on July 22, 2024 (the “Closing”). The Lexington Transaction was accounted for as a divestment of the Company’s commercial manufacturing activities in accordance with ASC 805, Business Combinations . ​ As consideration, the Company received (i) shares of newly issued Series C preferred stock of Genezen Holdings Inc. which are convertible into Genezen common stock and will accrue an 8.0 % per annum cumulative dividend, (ii) a convertible promissory note with a nominal amount of $ 12.5 million, bearing interest at 8.0 % per annum and maturing 63 months following the date of issuance, (iii) a right to purchase HEMGENIX at terms considered favorable to market terms and (iv) a firm purchase commitment liability for its customer contract with CSL Behring, inherently related to the right to purchase HEMGENIX. ​ Refer to Note 3 “ Divestiture of commercial manufacturing activities” and Note 4 “Other investments” for further information. ​ a. Series C preferred stock ​ The Company recorded the Series C preferred stock in Genezen Holdings Inc. issued to the Company at fair value. The Company subsequently measures these non-marketable equity securities at cost, less any impairment, adjusted to fair value if there are observable price changes in orderly transactions for an identical or similar investment in Genezen Holdings Inc., in accordance with topic ASC 321, Investments – Equity Securities. The series C preferred stock is presented within Other investments on the Company’s Consolidated Balance Sheets. ​ Refer to Note 4 “Other investments” for further information. ​ b. Convertible promissory note ​ The convertible promissory note was recognized at its fair value. The convertible promissory note is classified as not held for sale and subsequently measured at amortized cost, net of allowance for credit losses, as applicable, in accordance with topic ASC 310, Receivables, as it did not meet the definition of a debt security under topic ASC 320 , Investments – Debt Securities. Expected credit losses are determined with consideration to the financial condition and performance of the counterparty. The Company accrues interest income on its convertible promissory note using the effective interest method over the convertible promissory note’s contractual term. The convertible promissory note is presented within Other investments on the Company’s Consolidated Balance Sheets. ​ Refer to Note 4 “Other investments” for further information. ​ ​ 129 ​ Table of Contents c. Right to purchase ​ The Company entered into a Commercial Supply Agreement (the “CSA”) with Genezen. The CSA provides the Company with rights to purchase HEMGENIX at terms considered favorable to market terms. In accordance with ASC 805, Business Combinations, the Company recorded an intangible asset at its fair value with respect to these favorable terms at Closing. The intangible asset is stated at historical cost, less accumulated amortization. The Company amortizes the intangible asset on a straight-line basis over a three-year term. The Company presents the amortization expense within Other expense within the Consolidated Statements of Operations and Comprehensive Loss. ​ d. Firm purchase commitment liability ​ The CSA includes a minimum term of three years and minimum purchase commitments of HEMGENIX over the first three years , unless certain contractual provisions are triggered. The Company expects to resell HEMGENIX purchased from Genezen through its minimum commitments to CSL Behring at a loss. In accordance with ASC 330, Inventory, the Company recognized a liability related to the net losses expected from the purchase of these minimum commitments. The Company presents the current portion of the firm purchase commitment liability within Accrued expenses and other current liabilities and the non-current portion within Other non-current liabilities, net of current portion on the Consolidated Balance Sheets. The Company subsequently adjusts the liability for any changes to the losses expected to be incurred. The Company presents changes to the liability within Other expense within the Consolidated Statements of Operations and Comprehensive Loss. ​ 2.3.8 Notes to the Consolidated Statements of Cash Flows ​ The Consolidated Statements of Cash Flows have been prepared using the indirect method. The cash disclosed in the Consolidated Statements of Cash Flows is comprised of cash and cash equivalents and restricted cash. Cash and cash equivalents include bank balances, demand deposits and other short-term highly liquid investments (with maturities of less than three months at the time of purchase) that are readily convertible into a known amount of cash and are subject to an insignificant risk of fluctuation in value. ​ Cash flows denominated in foreign currencies have been translated at the average exchange rates. Exchange differences, if any, affecting cash and cash equivalents are shown separately in the Consolidated Statements of Cash Flows. Interest paid and received, and income taxes are included in net cash used in operating activities. ​ 2.3.9 Segment information ​ Operating segments are identified as a component of an enterprise for which separate discrete financial information is available for evaluation by the chief operating decision maker (“CODM”), or decision-making group, in making decisions on how to allocate resources and assess performance. The Company views its operations and manages its business as one operating segment, which comprises the discovery and development of innovative gene therapies. ​ 2.3.10 Net loss per ordinary share ​ The Company follows the provisions of ASC 260 , Earnings Per Share . In accordance with these provisions, net loss per ordinary share is calculated by dividing net loss by the weighted average number of ordinary shares outstanding during the period. ​ Diluted net loss per ordinary share reflects the dilution that would occur if share options or warrants to issue ordinary shares were exercised, performance or restricted share units were distributed, or shares under the employee share purchase plan were issued. However, potential ordinary shares are excluded if their effect is anti-dilutive. ​ Refer to Note 21 “ Basic and diluted earnings per share ” for further information. ​ 130 ​ Table of Contents 2.3.11 Impairment of long-lived assets ​ Long-lived assets, which include property, plant, and equipment and finite-lived intangible assets, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying value of an asset or asset group may not be recoverable. Right-of-use assets are also reviewed for impairment in accordance with ASC 360 , Property, Plant, and Equipment . The recoverability of the carrying value of an asset or asset group depends on the successful execution of the Company’s business initiatives and its ability to earn sufficient returns on approved products and product candidates. When events or changes in circumstances occur, the Company assesses recoverability by determining whether the carrying value of such assets will be recovered through the undiscounted expected future cash flows. If the future undiscounted cash flows are less than the carrying amount of these assets, the Company recognizes an impairment loss based on the excess of the carrying value over the fair value of the assets. Fair value is determined through various valuation techniques, including discounted cash flow models, quoted market values, and third-party independent appraisals, as considered necessary. ​ 2.3.12 Goodwill and acquired research and development intangible asset ​ a. Goodwill ​ Goodwill represents the excess of the fair value of the consideration transferred over the fair value of the net assets assumed in a business combination. Goodwill is not amortized but is evaluated for impairment on an annual basis, and between annual tests, if the Company becomes aware of any events occurring or changes in circumstances that would more likely than not reduce the fair value of the reporting unit below its carrying amount. A reporting unit is an operating segment or one level below an operating segment. In the years ended December 31, 2025, 2024 and 2023, the Company has not recognized any impairment charges related to goodwill. ​ b. Acquired research and development ​ As part of the uniQure France Acquisition, the Company recorded an In-process research and development intangible asset related to the AMT-260 program (the “IPR&D Intangible Asset”). The IPR&D Intangible Asset is considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts and is not amortized. If and when development is completed, which would occur when regulatory approval to market a candidate for the treatment of temporal lobe epilepsy is obtained, the associated asset would be deemed finite-lived and would then be amortized based on its respective useful life at that point in time. For the years ended December 31, 2025, 2024 and 2023, the Company has not recognized any impairment charges related to the IPR&D Intangible Asset. ​ In case of abandonment, the IPR&D Intangible Asset will be written off. In accordance with ASC 350, Intangibles – Goodwill and Other , the Company tests indefinite-lived intangible assets for impairment on an annual basis, and between annual tests, if the Company becomes aware of any events occurring or changes in circumstances that would indicate that the fair value of the IPR&D Intangible Asset is below its carrying amount. ​ 2.3.13 Investment securities ​ Investment securities consist of sovereign debt with residual maturities of less than 12 months (presented as current) and beyond (presented as non-current). The Company classifies these securities as held-to-maturity. Held-to-maturity securities are those securities in which the Company has the ability and intent to hold the security until maturity. Held-to-maturity securities are recorded at amortized cost, adjusted for applicable accrued interest and the amortization or accretion of premiums or discounts. Premiums and discounts are amortized or accreted over the term of the related held-to-maturity security as an adjustment to yield using the effective interest rate method. ​ Investment securities with original maturities of 90 days or less when purchased are presented within cash and cash equivalents (December 31, 2025: nil , December 31, 2024: $ 15.3 million). ​ A decline in the market value of any investment security below cost that is deemed to be other than temporary, results in a reduction in the carrying amount to fair value. The impairment is charged to operations and a new cost base for the security is established. Other-than-temporary impairment charges are included in interest and other income (expense), net. Interest income is recognized when earned. ​ 131 ​ Table of Contents Refer to Note 5 “ Investment securities ” for further information. ​ 2.3.14 Accounts receivable ​ Accounts receivables include amounts due from services provided to CSL Behring as well as unconditional rights to consideration from CSL Behring. ​ 2.3.15 Prepaid expenses ​ Prepaid expenses are amounts paid in the period, for which the benefit has not been realized, and include payments made for insurance and research and clinical contracts. The related expense will be recognized in the subsequent period as incurred. ​ 2.3.16 Other (non-) current assets ​ Deposits paid are either presented as Other current assets and receivables or as Other non-current assets based on the duration of the underlying contractual arrangement. Deposits are classified as restricted cash and primarily relate to facility leases. ​ Contract assets are presented in current assets or as non-current assets based on the timing of the right to consideration. ​ 2.3.17 Property, plant, and equipment ​ Property, plant, and equipment is comprised mainly of laboratory equipment, leasehold improvements, construction-in-progress (“CIP”) and office equipment. All property, plant and equipment is stated at cost, less accumulated depreciation. CIP consists of capitalized expenses associated with construction of assets not yet placed into service. Depreciation commences on CIP once the asset is placed into service based on its useful life determined at that time. ​ Maintenance and repairs that do not improve or extend the lives of the respective assets are expensed as incurred. Upon disposal, the related cost and accumulated depreciation is removed from the accounts and any resulting gain or loss on the transaction is recognized within the Consolidated Statements of Operations and Comprehensive Loss. ​ Depreciation is calculated using the straight-line method over the estimated useful lives of the assets (or in the case of leasehold improvements a shorter lease term), which are as follows: ​ ​ ​ ​ ​ ​ ​ · Leasehold improvements ​ ​ ​ Between 10 – 15 years · Laboratory equipment ​ 5 years · Office equipment ​ Between 3 – 5 years ​ 2.3.18 Leases ​ The Company records leases in accordance with ASC 842 , Leases and determines if an arrangement is a lease at inception. Operating lease right-of-use assets and lease liabilities are initially recognized based on the present value of future minimum lease payments over the lease term at commencement date calculated using an incremental borrowing rate applicable to the lease asset, unless the implicit rate is readily available. Lease terms may include options to extend or terminate the lease when it is reasonably certain that the Company will exercise that option. Leases with a term of twelve months or less are not recognized on the Consolidated Balance Sheets. The Company recognizes lease cost on a straight-line basis and presents these costs as operating expenses within the Consolidated Statements of Operations and Comprehensive Loss. The Company presents lease payments within cash flows from operations within the Consolidated Statements of Cash Flows. 132 ​ Table of Contents 2.3.19 Accounts payable and accrued expenses ​ Accounts payable comprise invoiced amounts related to obligations to pay for goods or services that have been acquired in the ordinary course of business from suppliers. Accounts payable are recognized at the amounts invoiced by suppliers. ​ Accrued expenses are recognized for goods or services that have been acquired in the ordinary course of business. ​ Contract liabilities, if any, are presented in accrued expenses. ​ 2.3.20 Long-term debt ​ Long-term debt is initially recognized at cost and presented net of original issue discount or premium and debt issuance costs on the Consolidated Balance Sheets. Amortization of debt discount and debt issuance costs is recognized as interest expense within the Consolidated Statements of Operations and Comprehensive Loss over the period of the debt, using the effective interest rate method. ​ 2.3.21 Pensions and other post-retirement benefit plans ​ The Company maintains a defined contribution pension plan for all employees in the Netherlands, which is funded by the Company through payments to an insurance company, with individual accounts for each participants’ assets. The Company has no legal or constructive obligation to pay further contributions if the plan does not hold sufficient assets to pay all employees the benefits relating to services rendered in the current and prior periods. The contributions are expensed as incurred. Prepaid contributions are recognized as an asset to the extent that a cash refund or a reduction in the future payments is available. ​ The Company maintains a qualified 401(k) Plan for all employees located in the U.S. The 401(k) Plan offers both a pre-tax and post-tax (Roth) component. Employees may contribute up to the U.S. Internal Revenue Service (“IRS”) statutory limit each calendar year. The Company matches $ 0.50 for every $ 1.00 contributed to the plan by participants, up to 6 % of base compensation. Employer contributions are recognized as they are contributed, as long as the employee is rendering services in that period. If employer contributions are made in periods after an individual retires or terminates, the estimated cost is accrued during the employee’s service period. ​ Expenses under the defined contribution plans were $ 1.8 million, $ 2.7 million and $ 3.6 million for the years ended December 31, 2025, 2024 and 2023, respectively. ​ The Company maintains a defined benefit plan for its Switzerland-based employees, including retirement benefit plans required by applicable local law. The Company accounts for pension assets and liabilities in accordance with ASC 715, Compensation - Retirement Benefits , which requires the recognition of the funded status of pension plans in the Company’s Consolidated Balance Sheets. The liability in respect to the defined benefit pension plan is the projected benefit obligation calculated annually by independent actuaries using the projected unit credit method. ​ The projected benefit obligations as of December 31, 2025 and December 31, 2024 represent the actuarial present value of the estimated future payments required to settle the obligation that is attributable to employee services rendered before that date. Service cost is reported in research and development and general and administrative expenses. All other components of net period costs are reported in interest expense within the Consolidated Statement of Operations and Comprehensive Loss. Plan assets are recorded at their fair value. Gains or losses arising from plan curtailments or settlements are accounted for at the time they occur. Actuarial gains and losses arising from differences between the actual and the expected return on plan assets are recognized in Accumulated other comprehensive loss. ​ ​ ​ ​ ​ 133 ​ Table of Contents 2.3.22 Share-based compensation ​ The Company accounts for its share-based compensation awards in accordance with ASC 718 , Compensation-Stock Compensation. ​ All of the Company’s share-based compensation plans for employees are equity-classified. ASC 718 requires all share-based compensation to employees, including grants of employee options, restricted share units, performance share units and modifications to existing instruments, to be recognized within the Consolidated Statements of Operations and Comprehensive Loss, based on their grant-date fair values, net of an estimated forfeiture rate, over the requisite service period. Forfeitures of employee options are recognized as they occur. Compensation expense related to Performance Share Units is recognized when the Company considers achievement of the associated milestones to be probable. The requirements of ASC 718 are also applied to non-employee share-based payment transactions except for specific guidance on certain inputs to an option-pricing model and the attribution of cost. ​ The Company uses a Hull & White option model to determine the fair value of option awards. The model captures early exercises by assuming that the likelihood of exercises will increase when the share price reaches defined multiples of the strike price. This analysis is performed over the full contractual term. ​ 2.3.23 Revenue recognition ​ The Company primarily generates revenue from its commercialization and license agreement with CSL Behring (the “CSL Behring Agreement”). ​ License revenue ​ In June 2020 the Company entered into the CSL Behring Agreement pursuant to which CSL Behring received the exclusive global rights to HEMGENIX, which became fully effective in May 2021. The Company concluded that CSL Behring is a customer in accordance with ASC 606 , Revenue from Contracts with Customers. The Company recognized the revenue related to its performance obligation to sell the exclusive global rights to HEMGENIX in May 2021. The Company also allocated the following consideration to this performance obligation: ​ i) Variable milestone payments; and, ii) Sales milestone payments and royalties ​ The Company recognizes license revenue in relation to the regulatory and sales milestone payments when it becomes probable that these will be achieved, and when royalties on sales of HEMGENIX have been earned. ​ Refer to Note 17 “ Collaboration arrangements and concentration of credit risk ” for further information. ​ Contract manufacturing revenue ​ In the period between April 2022 and July 2024, the Company manufactured HEMGENIX for CSL Behring in accordance with a June 2020 Development and Commercial Supply Agreement between the Company and CSL Behring. Following the Closing of the Lexington Transaction in July 2024, title to HEMGENIX drug product supply directly passes from the contract manufacturer, Genezen, to CSL Behring. The Company does not control HEMGENIX before it is transferred to CSL Behring. The Company arranges for HEMGENIX to be provided by Genezen to CSL Behring. The Company determined that it is an agent in the sale of HEMGENIX to CSL Behring with related accounts receivable presented in Other current assets and receivables in the Consolidated Balance Sheets. ​ The Company recognizes contract manufacturing revenue when ownership transferred to CSL Behring. Corresponding costs related to the purchase of HEMGENIX from Genezen, net of income from the sales of HEMGENIX to CSL Behring, as well as income related to the release of liabilities associated with expected net losses, in Other expense within the Company’s Consolidated Statements of Operations and Comprehensive Loss. ​ Collaboration revenue ​ Collaboration revenue related to contracted services is recognized when performance obligations are satisfied. ​ 134 ​ Table of Contents 2.3.24 Other income, other expense ​ The Company receives certain government and regional grants, which support its research efforts in defined projects, and include contributions towards the cost of research and development. These grants generally provide for reimbursement of approved costs incurred as defined in the respective grants and are deferred and recognized within the Consolidated Statements of Operations and Comprehensive Loss over the period necessary to match them with the costs they are intended to compensate, when it is probable that the Company has complied with any conditions attached to the grant and will receive the reimbursement. ​ 2.3.25 Research and development expenses ​ Research and development costs are expensed as incurred. Research and development expenses generally consist of laboratory research, clinical trials, statistical analysis, report writing, and regulatory compliance costs incurred with clinical research organizations and other third-party vendors (including post-approval commitments to conduct consistency and comparability studies). In addition, research and development costs include costs of materials and costs of intangible assets purchased from others for use in research and development activities. The costs of intangibles that are purchased from others for a particular research and development project and that have no alternative future use (in other research and development projects, or otherwise) are expensed as research and development costs at the time the costs are incurred or when it is identified that they have no alternative future use. ​ 2.3.26 Income taxes ​ Income taxes are recorded in accordance with ASC 740 , Income Taxes , which provides for deferred taxes using an asset and liability approach. The Company recognizes deferred tax assets and liabilities for the expected future tax consequences of events that have been included in the consolidated financial statements or tax returns. Deferred tax assets and liabilities are determined based on the difference between the consolidated financial statement carrying amount and the tax bases of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. Valuation allowances are provided, if based upon the weight of available evidence, it is more-likely-than-not that some or all of the deferred tax assets will not be realized. ​ The benefits of tax positions are recognized only if those positions are more likely than not, based on their technical merits, to be sustained upon examination. Recognized tax positions are measured at the largest amount of tax benefit that is greater than 50 percent likely of being realized upon settlement. The determination as to whether the tax benefit will more-likely-than-not be realized is based upon the technical merits of the tax position, as well as consideration of the available facts and circumstances. As of December 31, 2025, and 2024, the Company did not have any significant unrecognized tax benefits. ​ In accordance with ASC 740, Income Taxes , the Company has made an election to classify interest associated with income tax payments to tax authorities as interest expense. ​ 2.3.27 Royalty Financing Agreement ​ In May 2023, uniQure biopharma B.V. (“uniQure biopharma”), a wholly-owned subsidiary of the Company, entered into an agreement (the “Royalty Financing Agreement”) with HemB SPV, L.P. (the “Purchaser”) to sell certain current and future royalties due to uniQure biopharma from CSL Behring under the CSL Behring Agreement by and between uniQure biopharma and CSL Behring from the net sales of HEMGENIX. Refer to Note 12 “Royalty Financing Agreement” for further details of the Royalty Financing Agreement. The Company determined that the Royalty Financing Agreement should be accounted for as debt in accordance with topic ASC 470, Debt . The Company initially recognized the debt at fair value. The Company subsequently records the debt at amortized cost and determines the effective interest rate based on its projection of contractual cash flows. Interest expenses are presented as Interest expense within the Consolidated Statements of Operations and Comprehensive Loss, and are recorded over the projected repayment period using the effective interest method. The Company periodically assesses and adjusts the effective interest rate to reflect changes in projected cash flows. The Company prospectively applies the adjusted effective interest rate following the date of change. ​ 135 ​ Table of Contents In accordance with topic ASC 835, Interest , debt issuance costs incurred in relation to the Royalty Financing Agreement are presented as a reduction of the carrying amount of the debt. Debt issuance cost is amortized together with the interest expense recorded. ​ Interest expense, net of interest paid is presented as an adjustment to reconcile net loss to net cash used in operating activities within the Consolidated Statement of Cash Flows. ​ 2.3.28 Restructuring expenses ​ Restructuring charges consist of one-time termination benefits. The Company records one-time termination benefits in accordance with ASC 420, Exit or Disposal Cost Obligations . One-time termination benefits are expensed as of the date the Company notifies the employee, unless the employee must provide future service, in which case the benefits are expensed ratably over the future service period. ​ The Company recorded restructuring charges in accordance with ASC 712, Compensation—Nonretirement Postemployment Benefits when the terms offered were substantially similar to the terms recently offered. Under this standard, the Company recognizes a liability when the obligation is probable and can be estimated. The Company estimates the cost of these benefits and records a liability for the expected future payments. The liability is adjusted periodically to reflect changes in estimates, and related costs are recognized in the period incurred. ​ Other costs relate to the impairment of the Company’s research and development laboratory in Lexington which closed as a result of an October 2023 reorganization. The Company recognized an impairment loss of the right-of-use asset and corresponding leasehold improvements in accordance with ASC 360 , Property, Plant and Equipment . ​ 2.3.29 Recently Adopted Accounting Pronouncements ​ In the year ended December 31, 2025, the Company adopted ASU 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures . This update requires enhanced disaggregation and transparency of income tax disclosures, including expanded rate reconciliation and cash tax information. The adoption of ASU 2023-09 resulted in additional income tax disclosures included in this Annual Report on Form 10-K and did not have a material impact on the Company’s consolidated financial statements ​ In November 2024, the SEC adopted final rules under Release No. 33-11275, Disaggregation of Income Statement Expenses (ASU 2024-03) . The rules require registrants to provide enhanced disclosures regarding the disaggregation of certain operating expense categories. The new disclosures are required on an annual basis for fiscal years beginning after December 15, 2026 for large accelerated filers, and interim period disclosures are required beginning in the first quarterly report for the year after adoption. Early adoption is permitted. The Company is currently evaluating the impact of the final rules. ​ There are no other recently issued accounting pronouncements pending adoption that are applicable or expected to have a material impact on the Company. ​ 136 ​ Table of Contents 3. Divestiture of commercial manufacturing activities ​ On June 29, 2024, affiliates of the Company agreed with Genezen to sell the Company’s commercial manufacturing activities located in Lexington, MA. The Lexington Transaction closed on July 22, 2024. ​ Genezen extended offers of employment to a significant majority of the Company’s employees located at the Lexington facility (the “Lexington Facility”), with the remaining employees terminated effective August 30, 2024. ​ uniQure Inc. and uniQure biopharma, both wholly owned subsidiaries of the Company, entered into an Asset Purchase Agreement (“APA”) with Genezen on June 29, 2024. Pursuant to the APA, Genezen agreed to acquire the manufacturing facility including equipment and related manufacturing operations with a carrying value of $ 15.2 million, inventory with a carrying value of $ 8.8 million and certain other assets (including allocated goodwill) with a carrying value of $ 2.8 million associated with the Lexington Facility on Closing. ​ As consideration, the Company received (i) shares of newly issued Series C preferred stock of Genezen Holdings Inc. which are convertible into Genezen common stock and will accrue an 8.0 % per annum cumulative dividend, (ii) a convertible promissory note with a nominal amount of $ 12.5 million, bearing interest at 8.0 % per annum and maturing 63 months following the date of issuance and (iii) a right to purchase HEMGENIX at terms considered favorable to market terms. The Company also included a firm purchase commitment liability for its customer contract with CSL Behring, inherently related to the right to purchase HEMGENIX in the consideration received. Refer to Note 2.3.7 “ Divestiture of commercial manufacturing activities ” and Note 4 “ Other investments ”. ​ uniQure Inc., Genezen and the landlord of the Lexington Facility entered into an agreement for uniQure Inc. to assign and Genezen to assume the existing lease agreement between uniQure Inc. and the landlord at Closing. The Company also amended its original July 2013 guarantee to continue guaranteeing rental payments owed by Genezen through to the end of the current lease term in May 2029, under which, as of December 31, 2025, the Company remained obligated for lease payments of $ 16.3 million. In the event of Genezen’s default related to rental payments owed to the landlord, uniQure Inc. is entitled to terminate the assignment agreement and step into the original lease agreement. On Closing, the Company derecognized its right of use asset with a carrying amount of $ 11.8 million and related lease liability for the facility of $ 17.7 million. Following the Closing, $ 1.7 million of deposits were released and reclassified from restricted cash into cash. ​ At Closing, uniQure Inc. entered into the CSA with Genezen. Pursuant to the terms of the CSA, the parties agreed to subcontract the manufacturing of HEMGENIX to Genezen. The CSA includes a minimum term of three years and minimum purchase commitments of HEMGENIX commercial supplies of $ 43.3 million over the first three years , unless certain contractual provisions are triggered. The CSA provides the Company with rights to purchase HEMGENIX at terms considered favorable to market terms. In accordance with ASC 805 Business Combinations , the Company recorded an intangible asset valued at $ 16.7 million with respect to these favorable terms. The intangible asset will be amortized on a straight-line basis over a three-year term, commencing at Closing. Amortization expense of $ 5.6 million and $ 2.5 million (presented within Other expense within the Consolidated Statement of Operations and Comprehensive Loss) was recorded during the years ended December 31, 2025 and December 31, 2024, respectively. ​ The Company’s obligations with respect to the supply of HEMGENIX to CSL Behring pursuant to the Development and Commercial Supply Agreement between uniQure biopharma and CSL Behring Inc (the “DCSA”) remain in effect notwithstanding the subcontracting to Genezen. The Company expects to resell HEMGENIX material purchased from Genezen through its minimum commitments to CSL Behring at a loss. In accordance with ASC 330 Inventory , the Company, at Closing, recognized a liability of $ 8.8 million related to the net losses expected from the purchase of these minimum commitments. The liability was accounted for as a reduction of the consideration received. As of December 31, 2025, the Company classified $ 5.1 million (December 31, 2024: $ 1.6 million) of the liability as Accrued expenses and other current liabilities and $ 0.9 million (December 31, 2024: $ 4.8 million) within Other non-current liabilities, net of current portion within the Consolidated Balance Sheets. ​ The Lexington Transaction was accounted for as a divestment of the Company’s commercial manufacturing activities. The total net consideration received of $ 25.4 million, less costs associated with the sale of $ 3.3 million, exceeded the $ 20.9 million fair market value of the net assets transferred (including allocated goodwill) by $ 1.2 million. The excess over the fair market value was recognized as a net gain in Other income within the Consolidated Statement of Operations and Comprehensive Loss. 137 ​ Table of Contents ​ At Closing, the Company paid a total of $ 8.3 million to Genezen and CSL related to adjustments of working capital and to obtain consent to proceed with the divestiture. ​ Additionally, uniQure biopharma entered into a development and other manufacturing services agreement (“DMSA”) with Genezen at Closing. Pursuant to the DMSA, the Company is entitled to receive, as a preferred customer, manufacturing and development services to support the Company’s investigational gene therapy programs and other services related to HEMGENIX (other than its manufacturing and supply obligations under the CSA). The DMSA has a minimum term of three years and requires the Company to purchase services for a total minimum of $ 14.0 million. As of December 31, 2025, the remaining minimum purchase commitments amount to $ 7.3 million. ​ 4. Other investments ​ Convertible promissory note ​ The Company holds an investment in a convertible promissory note with a nominal amount of $ 12.5 million, bearing interest at 8.0 % per annum, for which Genezen is the counterparty. Refer to Note 3 “ Divestiture of commercial manufacturing activities” . The convertible promissory note was issued in July 2024 and matures in October 2029. The convertible promissory note had a balance of $ 14.6 million as of December 31, 2025 (December 31, 2024: $ 13.7 million) and is presented within Other investments in the Company’s Consolidated Balance Sheets. In the years ended December 31, 2025 and 2024, the Company recognized $ 1.0 million and $ 0.4 million of interest income, respectively, compared to nil in 2023. As of December 31, 2025, the Company has not recorded an allowance for credit losses related to the convertible promissory note. ​ Investments valued under measurement alternative ​ The Company holds investments in non-publicly traded equity securities without readily determinable fair values. These investments are accounted for at cost, less impairment and adjusted to fair value if there are observable price changes in orderly transactions for identical or similar investments using the measurement alternative in accordance with ASC 321, Investments – Equity Securities . The carrying value of these investments as of December 31, 2025 and December 31, 2024 was $ 15.6 million and $ 13.8 million, respectively, and are presented within Other Investments in the Company’s Consolidated Balance Sheets. The Company did not recognize any gains, losses, or impairments relating to investments carried under the measurement alternative in the years ended December 31, 2025, 2024 and 2023. ​ ​ 138 ​ Table of Contents 5. Investment securities The following table summarizes the Company’s investments in government debt securities as of December 31, 2025 and 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2025 ​ ​ ​ ​ Amortized cost ​ ​ ​ Gross unrealized holding gains ​ ​ ​ Gross unrealized holding losses ​ ​ ​ Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 542,301 ​ $ 308 ​ $ — ​ $ 542,609 Total ​ $ 542,301 ​ $ 308 ​ $ — ​ $ 542,609 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2024 ​ ​ ​ ​ Amortized cost ​ ​ ​ Gross unrealized holding gains ​ ​ ​ Gross unrealized holding losses ​ ​ ​ Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 208,591 ​ $ 164 ​ $ — ​ $ 208,755 Total ​ $ 208,591 ​ $ 164 ​ $ — ​ $ 208,755 ​ The Company invests in short-term U.S. and European government debt securities with high investment credit ratings. The U.S. and European government bonds are U.S. dollar and euro denominated, respectively. Expected credit losses on government debt securities are assessed based on their credit quality and historical default experience. As of December 31, 2025, no expected credit loss was identified with respect to the investment securities. Investment securities with original maturities of 90 days or less when purchased are presented within cash and cash equivalents and measured at amortized cost (December 31, 2025: nil , December 31, 2024: $ 15.3 million). Inputs to the fair value of the investments are considered Level 2 inputs. ​ ​ 6. Fair value measurement ​ The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ​ The carrying amount of cash and cash equivalents, accounts receivable from licensing and collaboration partners, other assets, accounts payable, accrued expenses and other current liabilities reflected in the Consolidated Balance Sheets approximate their fair values due to their short-term maturities. ​ The Company’s material financial assets include cash and cash equivalents, restricted cash and investment securities. Cash and cash equivalents and restricted cash are measured at fair value using Level 1 inputs. Restricted cash is included in Other non-current assets within the Consolidated Balance Sheets. Investment securities are measured at amortized cost. ​ Contingent consideration ​ The Company is required to pay up to EUR 143.1 million ($ 168.1 million at the December 31, 2025 foreign exchange rate) to the former shareholders of uniQure France upon the achievement of the remaining contractually defined milestones in connection with the uniQure France Acquisition. ​ The fair value of the contingent consideration liability related to the uniQure France Acquisition as of December 31, 2025 was $ 18.7 million (December 31, 2024: $ 10.9 million) using a discount rate of 11.8 % (December 31, 2024: 15.3 % to 16.2 %). 139 ​ Table of Contents ​ In December 2024, a milestone payment of EUR 30.0 million ($ 31.5 million) was paid, of which EUR 26.8 million ($ 28.2 million) related to contingent consideration. No milestones were achieved or paid during the year ended December 31, 2025. ​ The following table sets forth the balances and changes in fair values of the contingent consideration liability, which is measured at fair value using Level 3 inputs: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent ​ ​ ​ ​ consideration ​ ​ (in thousands) Balance at December 31, 2022 ​ $ 35,316 Changes in fair value of contingent consideration ​ ​ 15,895 Contingent consideration milestone payments ​ ​ ( 9,563 ) Currency translation effects ​ ​ 1,358 Balance at December 31, 2023 ​ $ 43,006 Changes in fair value of contingent consideration ​ ​ ( 1,817 ) Contingent consideration milestone payments ​ ​ ( 28,167 ) Currency translation effects ​ ​ ( 2,162 ) Balance at December 31, 2024 ​ $ 10,860 Changes in fair value of contingent consideration ​ ​ 6,247 Currency translation effects ​ ​ 1,629 Balance at December 31, 2025 ​ $ 18,736 ​ If, as of December 31, 2025, the Company had assumed a 100 % likelihood of AMT-260 advancing into a Phase III clinical study, then the fair value of the contingent consideration would have increased to EUR 51.4 million ($ 60.4 million). If, as of December 31, 2025 the Company had assumed that it would discontinue development of the AMT-260 program, then the contingent consideration would have been released to income. ​ As of December 31, 2025, the Company classified none of the total contingent consideration of $ 18.7 million as current liabilities. The balance sheet classification between current and non-current liabilities is based upon the Company’s best estimate of the timing of settlement of the remaining relevant milestones. ​ Liability related to pre-funded warrants ​ In September 2025, the Company completed a follow-on public offering which included the issuance of Pre-Funded Warrants to purchase 526,316 of the Company’s ordinary shares at the public offering price of $ 47.50 per ordinary share, less a $ 0.0001 per ordinary share exercise price for each Pre-Funded Warrant. The obligation to issue ordinary shares upon the exercise of the Pre-Funded Warrants is classified as a liability related to pre-funded warrants. The liability related to pre-funded warrants is accounted for at fair value in accordance with ASC 820, Fair Value Measurement , with the total gross proceeds received with respect to the Pre-Funded Warrants determined as reflective of the fair value of the obligation on the date of issuance. Changes in the fair value of the liability related to pre-funded warrants are recognized within Other non-operating gains, net of issuance costs, within the Company’s Consolidated Statements of Operations and Comprehensive Loss. ​ The Pre-Funded Warrants are not exchange-quoted and are measured using a valuation technique whose significant inputs are observable; therefore, the fair value measurement is classified within Level 2 of the fair value hierarchy. During the year ended December 31, 2025 no warrants were exercised. ​ ​ ​ ​ ​ ​ ​ Liability related ​ ​ to pre-funded ​ ​ warrants ​ ​ ​ 2025 ​ ​ (in thousands) Balance at December 31, 2024 ​ $ — Issuance of pre-funded warrants in connection with follow-on public offering ​ ​ 25,000 Unrealized change in fair value ​ ​ ( 12,405 ) Balance at December 31, 2025 ​ $ 12,595 ​ 140 ​ Table of Contents Investment securities ​ Refer to Note 5 “ Investment securities ” for the fair value of the investment securities as of December 31, 2025. ​ Pension plan assets ​ Refer to Note 13 “ Retirement benefits ” for the fair value of the plan assets as of December 31, 2025. ​ ​ ​ 7. Property, plant, and equipment, net ​ The following table presents the Company’s property, plant, and equipment as of December 31, 2025 and 2024, respectively: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ (in thousands) Leasehold improvements ​ $ 28,188 ​ $ 24,808 Laboratory equipment ​ ​ 24,990 ​ ​ 23,359 Office equipment ​ ​ 4,358 ​ ​ 3,913 Total property, plant, and equipment ​ ​ 57,536 ​ ​ 52,080 Less accumulated depreciation ​ ​ ( 43,736 ) ​ ​ ( 31,656 ) Property, plant and equipment, net ​ $ 13,800 ​ $ 20,424 ​ Total depreciation expense was $ 9.1 million for the year ended December 31, 2025 (December 31, 2024: $ 10.1 million). Depreciation expense is allocated to Research and development expense and Cost of contract manufacturing within the Consolidated Statement of Operations and Comprehensive Loss, to the extent it related to the Company’s commercial manufacturing facility and equipment and laboratory equipment. All other depreciation expenses are allocated to Selling, general and administrative expense. ​ During the year ended December 31, 2024, the Company sold property, plant and equipment with a carrying value of $ 15.2 million, including leasehold improvements with a carrying value of $ 6.4 million, laboratory and office equipment with a carrying value of $ 6.0 million, as well as assets under construction with a carrying value of $ 2.8 million as part of the Lexington Transaction (refer to Note 3 “ Divestment of commercial manufacturing activities” ). ​ The following table summarizes property, plant, and equipment balances by geographic region as of December 31, 2025 and 2024, respectively: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ December 31, ​ ​ 2025 ​ 2024 ​ ​ (in thousands) Dutch sites ​ $ 13,154 ​ $ 19,463 Lexington, Massachusetts (U.S.) ​ 461 ​ 730 Other ​ ​ 185 ​ ​ 231 Total ​ $ 13,800 ​ $ 20,424 ​ ​ 8. Right-of-use asset and lease liabilities ​ The Company’s most significant leases relate to office and laboratory space under the following operating lease agreements: ​ Lexington, Massachusetts / U.S. ​ In February 2022, the Company entered into a lease for an office facility in Lexington, Massachusetts, U.S. of 12,716 square feet. The lease commenced in December 2022 and is set for a non-cancellable period ending March 2030. The lease is renewable for one five-year term. ​ 141 ​ Table of Contents In December 2021, the Company entered into a lease for a research and development facility in Lexington, Massachusetts, U.S. of 13,501 square feet. The lease commenced in May 2022 and is set for a non-cancellable period ending March 2029. Commencing August 2024, the Company subleased this facility for the residual term. The fixed lease payments to be received during the remaining term under the agreement to sublease amount to $ 2.5 million as of December 31, 2025. Amsterdam / The Netherlands ​ In March 2016, the Company entered into a 16-year lease for a facility in Amsterdam, the Netherlands and amended this agreement in June 2016. The lease for the facility terminates in February 2032, with an option to extend in increments of five-year periods. The lease contract includes variable lease payments related to annual increases in payments based on a consumer price index. In May 2021, the Company leased an additional approximately 1,080 square meters of office space. The lease expires in October 2028. ​ As of December 31, 2025 the Company is sub-leasing two of the seven floors of its Amsterdam facility for a ten-year term ending on December 31, 2027. ​ The fixed lease payments to be received during the remaining term under the agreement to sub-lease amount to EUR 1.9 million ($ 2.2 million) as of December 31, 2025. ​ Operating lease liabilities ​ The components of lease cost for the years ended December 31, 2025, 2024 and 2023, respectively, were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Operating lease cost ​ $ 7,152 ​ $ 6,486 ​ $ 7,018 Variable lease cost ​ ​ 871 ​ ​ 1,137 ​ ​ 1,238 Sublease income ​ ​ ( 1,540 ) ​ ​ ( 1,162 ) ​ ​ ( 957 ) Total lease cost ​ $ 6,483 ​ $ 6,461 ​ $ 7,299 ​ The table below presents the lease-related assets and liabilities recorded in the Consolidated Balance Sheets, as of December 31, 2025 and 2024, respectively: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ (in thousands) Assets ​ ​ ​ ​ ​ ​ Operating lease right-of-use assets ​ $ 12,525 ​ $ 13,647 Liabilities ​ ​ ​ ​ ​ ​ Current ​ ​ ​ ​ ​ ​ Current operating lease liabilities ​ ​ 3,862 ​ ​ 3,601 Non-current ​ ​ ​ ​ ​ ​ Non-current operating lease liabilities ​ ​ 9,832 ​ ​ 11,136 Total lease liabilities ​ $ 13,694 ​ $ 14,737 ​ Other information The weighted-average remaining lease term as of December 31, 2025, is 5.1 years, compared to 5.9 years as of December 31, 2024, and the weighted-average discount rate as of December 31, 2025 is 11.5 % , compared to 11.3 % as of December 31, 2024. The Company uses an incremental borrowing rate applicable to the lease asset. ​ 142 ​ Table of Contents The table below presents supplemental cash flow and non-cash information related to leases for the years ended December 31, 2025, 2024 and 2023, respectively: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Cash paid for amounts included in the measurement of lease liabilities ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating cash flows for operating leases ​ $ 8,269 ​ $ 6,113 ​ $ 7,921 ​ Undiscounted cash flows The table below reconciles the undiscounted cash flows as of December 31, 2025, for each of the five following years and the total of the remaining years, to the operating lease liabilities recorded in the Consolidated Balance Sheet as of December 31, 2025. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amsterdam (1) ​ ​ ​ Lexington ​ ​ ​ Other (2) ​ ​ ​ Total ​ ​ (in thousands) 2026 ​ $ 2,188 ​ ​ 1,431 ​ ​ 247 ​ ​ 3,866 2027 ​ ​ 2,192 ​ ​ 1,469 ​ ​ — ​ ​ 3,661 2028 ​ ​ 2,112 ​ ​ 1,508 ​ ​ — ​ ​ 3,620 2029 ​ ​ 1,982 ​ ​ 763 ​ ​ — ​ ​ 2,745 2030 ​ ​ 1,982 ​ ​ 130 ​ ​ — ​ ​ 2,112 Thereafter ​ ​ 1,817 ​ ​ — ​ ​ — ​ ​ 1,817 Total lease payments ​ $ 12,273 ​ $ 5,301 ​ $ 247 ​ $ 17,821 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Less: amount of lease payments representing interest payments ​ ​ ( 3,268 ) ​ ​ ( 859 ) ​ ​ — ​ ​ ( 4,127 ) Present value of lease payments ​ ​ 9,005 ​ ​ 4,442 ​ ​ 247 ​ ​ 13,694 Less: current operating lease liabilities ​ ​ ( 2,188 ) ​ ​ ( 1,427 ) ​ ​ ( 247 ) ​ ​ ( 3,862 ) Non-current operating lease liabilities ​ $ 6,817 ​ $ 3,015 ​ $ — ​ $ 9,832 (1) Payments are due in EUR and have been translated at the foreign exchange rate as of December 31, 2025, of $ 1.18 / €1.00 (2) Payments are due in CHF and have been translated at the foreign exchange rate as of December 31, 2025, of $ 1.26 / CHF1.00 ​ 9. Intangible assets, net and Goodwill ​ The following table presents the Company’s acquired licenses, intangible asset related to the favorable supply terms under the CSA and Acquired IPR&D Intangible Asset as of December 31, 2025 and 2024, respectively: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2025 ​ ​ ​ ​ Gross Carrying Amount ​ ​ ​ Accumulated Amortization ​ ​ ​ Net ​ ​ (in thousands) Acquired licenses ​ $ 2,576 ​ $ ( 1,402 ) ​ $ 1,174 Favorable supply terms under CSA ​ ​ 16,700 ​ ​ ( 8,021 ) ​ ​ 8,679 Total amortizable intangible assets ​ ​ 19,276 ​ ​ ( 9,423 ) ​ ​ 9,853 Acquired IPR&D Intangible Asset ​ ​ 62,937 ​ ​ — ​ ​ 62,937 Total intangible assets ​ $ 82,213 ​ $ ( 9,423 ) ​ $ 72,790 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2024 ​ ​ ​ ​ Gross Carrying Amount ​ ​ ​ Accumulated Amortization ​ ​ ​ Net ​ ​ (in thousands) Acquired licenses ​ $ 2,276 ​ $ ( 1,117 ) ​ $ 1,159 Favorable supply terms under CSA ​ ​ 16,700 ​ ​ ( 2,454 ) ​ ​ 14,246 Total amortizable intangible assets ​ ​ 18,976 ​ ​ ( 3,571 ) ​ ​ 15,405 Acquired IPR&D Intangible Asset ​ ​ 55,638 ​ ​ — ​ ​ 55,638 Total intangible assets ​ $ 74,614 ​ $ ( 3,571 ) ​ $ 71,043 ​ 143 ​ Table of Contents As of December 31, 2025, the estimated future amortization expense for each of the five succeeding years and the period thereafter is as follows: ​ ​ ​ ​ ​ Years ​ ​ ​ Amount ​ ​ (in thousands) 2026 ​ $ 5,705 2027 ​ 3,250 2028 ​ 138 2029 ​ 138 2030 ​ 138 Thereafter ​ 484 Total ​ $ 9,853 ​ a. Acquired licenses ​ All acquired licenses are owned by uniQure biopharma. The remaining weighted average life is 8.5 years as of December 31, 2025 (December 31, 2024: 9.5 years). ​ The amortization expense related to acquired licenses for the year ended December 31, 2025 was $ 0.1 million (December 31, 2024: $ 0.1 million and December 31, 2023: $ 0.1 million). ​ b. Favorable supply terms under the CSA ​ As part of the Lexington Transaction, the Company recognized an intangible asset related to its rights to purchase HEMGENIX at terms considered favorable to market terms. Refer to Note 3 “ Divestment of commercial manufacturing activities”. The intangible asset is amortized on a straight line basis over a three-year period that commenced in July 2024. ​ The amortization expense related to the intangible asset for the year ended December 31, 2025 was $ 5.6 million (December 31, 2024: $ 2.5 million and December 31, 2023: nil ). ​ c. Acquired in-process research and development ​ The IPR&D Intangible Asset was recorded as part of the uniQure France Acquisition. Refer to Note 2.3.12 “ Goodwill and acquired research and development intangible asset ”. ​ d. Goodwill ​ The goodwill was recorded as part of the uniQure France Acquisition. Refer to Note 2.3.12 “ Goodwill and acquired research and development intangible asset ”. ​ 10. Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items, as of December 31, 2025 and 2024, respectively: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ (in thousands) Accruals for goods received from and services provided by vendors-not yet billed ​ $ 20,490 ​ ​ 10,109 Personnel-related accruals and liabilities ​ ​ 9,941 ​ $ 12,290 Liability owed to the Purchaser pursuant to the Royalty Financing Agreement (refer to Note 12 " Royalty Financing Agreement ") ​ ​ 5,523 ​ ​ 4,951 Current portion of firm purchase commitment liability (refer to Note 3 " Divestiture of commercial manufacturing activities ") ​ ​ 5,102 ​ ​ 1,582 Other current liabilities ​ ​ 236 ​ ​ 293 Total ​ $ 41,292 ​ $ 29,225 ​ ​ 144 ​ Table of Contents 11. Long-term debt ​ On June 14, 2013, the Company entered into a venture debt loan facility with Hercules Capital, Inc. (“Hercules”). The facility has been amended at various times, including on July 22, 2024 (the “2024 Amended Facility”) and most recently on September 22, 2025 (the “2025 Amended Facility”), upon which date the amendment closed (the “Amendment Closing Date”). ​ On the Amendment Closing Date, the Company drew down $ 50.0 million of the 2025 Amended Facility to repay the $ 50.0 million then outstanding under the 2024 Amended Facility. A facility charge of $ 0.2 million was incurred on the Amendment Closing Date. The 2024 Amended Facility was due on January 7, 2027 and bore interest at a rate equal to the greater of (i) 7.95 % and (ii) 7.95 % plus the prime rate less 3.25 % per annum, reflecting a floating rate of 11.95 % at the Amendment Closing Date. ​ Pursuant to the 2025 Amended Facility, additional term loans of $ 125.0 million were made available. The Company may draw down (i) an additional $ 100.0 million in two increments of at least $ 25.0 million, following the approval of a Biologics License Application (“BLA”) for AMT-130 prior to June 15, 2027, provided that confirmatory trials to the extent and in the manner required to support full approval (if applicable) remain ongoing or are being planned, and (ii) an additional $ 25.0 million in a single advance, subject to approval by Hercules. Advances under the 2025 Amended Facility bear interest at a rate equal to the greater of (i) 9.45 % and (ii) the sum of the prime rate and 2.45 % , reflecting a floating rate of 9.45 % as per December 31, 2025. ​ The 2025 Amended Facility matures on October 1, 2030, upon which date the Company is required to repay the principal balance and any unpaid interest on advances received. The interest-only period of the 2025 Amended Facility is effective through October 1, 2028. The interest-only period will be extended to October 1, 2029 if the BLA for AMT-130 is approved prior to June 15, 2027. The 2025 Amended Facility will be interest-only if certain commercial milestones are met prior to December 31, 2028. ​ The Company may prepay all or part of the outstanding principal together with a prepayment charge of 1.50 % if repayment occurs within the first 30 months following the Amendment Closing Date, and thereafter, with a prepayment charge of 0.75 %. An end-of-term charge of 2.75 % of the aggregate principal outstanding is due if repaid within 18 months of the Amendment Closing Date, otherwise 5.50 % if repaid thereafter. ​ The total principal outstanding as of December 31, 2025 under the 2025 Amended Facility was $ 50.0 million. The amortized cost, including interest due presented as part of Accrued expenses and other current liabilities, was $ 50.1 million as of December 31, 2025, compared to $ 51.9 million as of December 31, 2024, and is recorded net of discount and debt issuance costs. The foreign currency gain on the loan facility for the year ended December 31, 2025 was $ 9.3 million, compared to a foreign currency loss of $ 4.1 million for the year ended December 31, 2024. The fair value of the loan approximates its carrying amount. Inputs to the fair value of the loan are considered Level 3 inputs. ​ Interest expense recorded during the years ended December 31 was as follows: ​ ​ ​ ​ ​ Years ​ ​ ​ Amount ​ ​ (in millions) 2025 ​ $ 6.9 2024 ​ 12.9 2023 ​ ​ 14.6 ​ 145 ​ Table of Contents Under the 2025 Amended Facility, the Company must remain current in its periodic reporting requirements. Unless the Company maintains a minimum market capitalization threshold of at least $ 1,200.0 million, the Company, beginning January 1, 2027, is required at all times to keep a minimum cash balance deposited in bank accounts in the U.S. of at least the lesser of (i) 65 % of the outstanding balance of aggregate principal due, provided that such percentage will be reduced to 50 % upon the occurrence of the approval of a BLA for AMT-130 prior to June 15, 2027, and further reduced to 35 % upon the occurrence of the contractually defined commercial milestones or (ii) 100 % of worldwide cash and cash equivalents. The 2025 Amended Facility also provides for a certain performance covenant related to AMT-130 net product revenue which would apply nine months past a potential BLA approval of AMT-130, unless the Company maintains a minimum market capitalization threshold of at least $ 1,200.0 million. The 2025 Amended Facility restricts the Company’s ability, among other things, to incur future indebtedness and obtain additional debt financing, make investments in securities or in other companies, transfer assets, perform certain corporate changes, own or hold certain digital assets, make loans to employees, officers, and directors, and make dividend payments and other distributions to its shareholders. The 2025 Amended Facility is secured by a direct or indirect pledge of the Company’s total assets of $ 824.9 million, less $ 35.5 million of cash and cash equivalents and other current assets held by the Company, and $ 88.8 million of other current assets and investments held by uniQure France SAS as well as receivables sold to HemB SPV, L.P. as described in Note 12 “ Royalty Financing Agreement ”. In accordance with the 2025 Amended Facility, the Company was in compliance with all applicable covenants as of December 31, 2025. ​ The aggregate maturities of the loan, including $ 21.9 million of coupon interest payments and financing fees, for each of the 58 months after December 31, 2025, are as follows: ​ ​ ​ ​ ​ Years ​ ​ ​ Amount ​ ​ (in thousands) 2026 ​ $ 4,791 2027 ​ ​ 5,416 2028 ​ ​ 10,243 2029 ​ ​ 26,534 2030 ​ ​ 24,938 Total ​ $ 71,922 ​ ​ ​ 12. Royalty Financing Agreement ​ In May 2023, the Company entered into the Royalty Financing Agreement with the Purchaser. Under the terms of the Royalty Financing Agreement, the Company received an upfront payment of $ 375.0 million in exchange for its rights to the lowest royalty tier on CSL Behring’s worldwide net sales of HEMGENIX for certain current and future royalties due to the Company. The Company will be obligated to pay $ 25.0 million of the first worldwide sales milestone payment from CSL Behring, if received, to the Purchaser. ​ The Purchaser will receive 1.85 times the upfront payment (or $ 693.8 million) until June 30, 2032 (“First Hard Cap Date”) if such thresholds are met or, if such cap is not met by June 30, 2032, up to 2.25 times of the upfront payment through December 31, 2038 (“Second Hard Cap Date”). If, on or prior to the defined dates for each cap amount, the total amount of royalty payments received by the Purchaser equals or exceeds the cap amount applicable to such date, the Royalty Financing Agreement will automatically terminate and all rights to the HEMGENIX royalty payments will revert back to the Company. The Company has no obligation to repay any amounts received from the Purchaser in the event that the applicable cap amount is not reached during the term of the Royalty Financing Agreement. ​ The Company has retained the rights to all other royalties, as well as commercial milestones totaling up to $ 1.3 billion, under the terms of the CSL Behring Agreement. ​ Net proceeds from the Royalty Financing Agreement, after deducting professional and financial advisory fees related to the transaction of $ 4.9 million, were $ 370.1 million. The Company initially recorded these net proceeds as a Liability from royalty financing agreement at their fair market value on its Consolidated Balance Sheet as of closing of the transaction on June 5, 2023. Following the initial recognition, the Company records the debt at amortized cost. 146 ​ Table of Contents As of December 31, 2025 the Company expects to satisfy its commitment to the Purchaser prior to the Second Hard Cap Date. The Company records the difference of $ 473.7 million between the total expected payments of $ 843.8 million to the Purchaser and the $ 370.1 million net proceeds as interest expense over the term using the effective interest rate method. The Company determined the effective interest rate based on the projected cash flows up to the Second Hard Cap Date. As of December 31, 2025 the effective interest rate is expected to be within a range of 10.5 % to 12.0 % per annum, compared to a range of 12.0 % to 13.5 % per annum as of December 31, 2024. The Company would have recorded the following amounts of interest expense if it had used the effective interest rate at the lower and upper end of this range: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ ​ 2023 ​ ​ ​ (in millions) Interest expense at effective interest rate of 10.5 % per annum for the year ended December 31, 2025, and 12.0 % per annum for the years ended December 31, 2024 and 2023. ​ $ 54.0 ​ $ 50.7 ​ $ 26.5 Interest recorded in the Consolidated Statements of Operations and Comprehensive Loss ​ ​ 54.1 ​ ​ 50.9 ​ ​ 26.9 Interest expense at effective interest rate of 12.0 % per annum for the year ended December 31, 2025, and 13.5 % per annum for the years ended December 31, 2024 and 2023. ​ ​ 54.6 ​ ​ 57.8 ​ ​ 29.9 ​ The Liability from royalty financing agreement was initially recognized at fair value and inputs were considered Level 3 inputs. ​ The following table presents the movement in the Liability from royalty financing agreement between the years ended December 31, 2023 and December 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ Amount of liability ​ ​ (in thousands) Balance as of December 31, 2023 (includes $ 1.4 million presented as "Accrued expenses and other current liabilities") ​ $ 395,678 Royalty payments to the Purchaser ​ ​ ( 6,662 ) Interest expense for the period ​ ​ 50,865 Balance as of December 31, 2024 (includes $ 5.0 million presented as "Accrued expenses and other current liabilities") ​ ​ 439,881 Royalty payments to the Purchaser ​ ​ ( 15,258 ) Interest expense for the period ​ ​ 54,099 Balance as of December 31, 2025 (includes $ 5.5 million presented as "Accrued expenses and other current liabilities") ​ $ 478,722 ​ ​ ​ 13. Retirement benefits ​ The Company operates a defined benefit pension plan for its Switzerland-based employees (the “Swiss Plan”) in accordance with local regulations and practices. The normal retirement age under the Swiss Plan is 65 years. All benefits are immediately vested. Under the Swiss Plan, a percentage of pensionable salary is contributed as a retirement credit with additional contributions being made for death and disability benefits. Under Swiss pension law, participants who are covered by the pension plan of another employer are required to transfer the termination benefit of that pension plan into the plan of the Company. When employment at the Company ends before reaching retirement, the termination benefit is transferred out of the defined benefit pension plan. At time of retirement, the accumulated retirement credit can be converted into a life-long annuity or be paid-out as a lump-sum. Participants are also permitted to withdraw a part of the accumulated termination benefit in special circumstances before reaching retirement age, for example for payments related to obtaining home ownership. ​ 147 ​ Table of Contents A summary of the changes in the projected benefit obligation and plan assets is presented below: ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ ​ 2025 ​ ​ (in thousands) Beginning projected benefit obligation ​ $ 11,495 Service cost ​ ​ 674 Interest cost ​ ​ 123 Contributions by the employees ​ ​ 633 Actuarial losses ​ ​ ( 600 ) Liabilities assumed from participants joining and leaving the plan, net ​ ​ 1,105 Foreign currency exchange rate changes ​ ​ 1,727 Ending projected benefit obligation ​ $ 15,157 ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ ​ (in thousands) Beginning fair value of plan assets ​ $ 9,500 Return on plan assets ​ ​ 22 Interest income ​ ​ 207 Contributions by the employer ​ ​ 633 Contributions by the employees ​ ​ 633 Assets contributed to the plan from participants joining and leaving the plan, net ​ ​ 1,105 Foreign currency exchange rate changes ​ ​ 1,474 Ending fair value of plan assets ​ $ 13,574 ​ Amounts recognized within the Consolidated Balance Sheets, presented within Other non-current liabilities, were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ (in thousands) Fair value of plan assets ​ $ 13,574 ​ $ 9,500 Present value of projected benefit obligation ​ ​ ( 15,157 ) ​ ​ ( 11,495 ) Funded status: (net liability) ​ $ ( 1,583 ) ​ $ ( 1,995 ) ​ ​ ​ ​ ​ ​ ​ Accumulated benefit obligation as of December 31 ​ $ 14,870 ​ $ 11,075 ​ Amounts recorded within Accumulated other comprehensive loss: ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2025 ​ ​ ​ ​ (in thousands) Actuarial loss - beginning of year ​ $ 2,157 Actuarial (gain) of current year ​ ​ ( 558 ) Amortization of prior service costs ​ ​ ( 206 ) Total ​ $ 1,393 ​ 148 ​ Table of Contents Net pension expense related to the defined benefit plans included the following components: ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2025 ​ ​ ​ ​ (in thousands) Service cost ​ $ 674 Interest cost ​ ​ 123 Interest income ​ ​ ( 207 ) Amortization of net loss ​ ​ 115 Gain/(loss) due to settlement ​ ​ 116 Net pension expense ​ $ 821 ​ The assumptions related to the Swiss Plan are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, Actuarial assumptions (% p.a.) ​ ​ ​ 2025 ​ ​ ​ 2024 Discount rate ​ ​ 1.30 % ​ ​ 0.90 % Expected return on plan assets ​ ​ 1.80 % ​ ​ 1.80 % Expected inflation rate ​ ​ 0.70 % ​ ​ 0.70 % Interest credit rate ​ ​ 1.25 % ​ ​ 1.25 % Long-term expected rate of salary increases ​ ​ 0.70 % ​ ​ 0.70 % Pension increase ​ ​ 0.00 % ​ ​ 0.00 % ​ As of December 31, 2025, the expected future cash flows in respect of the Swiss Plan were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ (in thousands) Year 1 ​ $ 622 ​ $ 490 Year 2 ​ ​ 510 ​ ​ 409 Year 3 ​ ​ 538 ​ ​ 417 Year 4 ​ ​ 593 ​ ​ 440 Year 5 ​ ​ 1,250 ​ ​ 480 Next 5 years ​ ​ 6,143 ​ ​ 4,747 ​ ​ ​ ​ ​ ​ ​ Other disclosure items: ​ ​ ​ ​ ​ ​ Next year's expected employer contribution ​ $ 669 ​ $ 575 ​ ​ ​ ​ ​ ​ ​ ​ The Company's investment strategy for its pension plan is to optimize the long-term investment return on plan assets in relation to the liability structure to maintain an acceptable level of risk while minimizing the cost of providing pension benefits and maintaining adequate funding levels in accordance with the applicable rules in each jurisdiction. The Company does not manage any assets internally. Plan assets represent assets held by the Swiss pension foundations in which the Company’s pension plan participates. ​ The allocation of plan assets is presented below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 Bonds ​ ​ 61 % ​ ​ 61 % Equities ​ ​ 26 % ​ ​ 25 % Real estate ​ ​ 10 % ​ ​ 10 % Others ​ ​ 3 % ​ ​ 4 % ​ The fair value of the plan assets is determined based on Level 2 inputs. ​ 149 ​ Table of Contents 14. Shareholders’ equity / (deficit) ​ As of December 31, 2025, the Company’s authorized share capital is EUR 4.0 million (or $ 4.7 million when translated at an exchange rate as of December 31, 2025, of $ 1.175 / €1.00), divided into 80,000,000 ordinary shares, each with a nominal value of € 0.05 . ​ All ordinary shares issued by the Company were fully paid. The minimum amount of share capital to be held under Dutch law is EUR 0.0 million. Under the Company’s Articles of Association, the Company is required to maintain a minimum amount of share capital in reserve. In addition, the Company is only permitted to make distributions on its ordinary shares to the extent that its Shareholders’ equity / (deficit) exceeds the sum of the paid-up and called-up capital and the reserves it is required to maintain under Dutch law. There are no other distribution restrictions applicable to the Company’s ordinary shares or Pre-Funded Warrants. ​ In January 2025, the Company received net proceeds of $ 70.1 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company, through a follow-on public offering of 4.4 million ordinary shares at a public offering price of $ 17.00 per ordinary share. In February 2025, the Company received an additional $ 10.4 million in net proceeds after related offering expenses upon the underwriters’ exercise of their option to purchase an additional 0.7 million ordinary shares at the public offering price. ​ In July 2025, the Company entered into a Sales Agreement with Leerink Partners LLC (“Leerink Partners”) with respect to an at-the-market (“ATM”) offering program, under which the Company may, from time to time and at the Company’s sole discretion, offer and sell through Leerink Partners, acting as agent, the Company’s ordinary shares, up to an aggregate offering of $ 200.0 million. As of December 31, 2025, no sales have been made under the ATM offering program. ​ In September 2025, the Company received net proceeds of $ 323.7 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company, through a follow-on public offering of 6.7 million ordinary shares, at a public offering price of $ 47.50 per ordinary share, and, in lieu of ordinary shares to certain investors, Pre-Funded Warrants to purchase 0.5 million of the Company’s ordinary shares at the public offering price less a $ 0.0001 per ordinary share exercise price. The Company has authorized and reserved a sufficient number of ordinary shares to permit the full exercise of all outstanding Pre-Funded Warrants. The Pre-Funded Warrants are classified as a liability. ​ During 2025, as a result of the Company’s revised Dutch corporate income tax filing positions for 2021 and 2023, the Company released $ 15.7 million of valuation allowance related to net operating loss carryforwards. The portion of the resulting tax benefit attributable to net operating loss carryforwards arising from 2019 share issuance costs was recorded in additional paid-in capital, increasing additional paid-in capital by $ 0.5 million for the year ended December 31, 2025. ​ 15. Share-based compensation ​ The Company’s share-based compensation plans include the amended and restated 2014 Share Incentive Plan (as amended, the “2014 Plan”) and inducement grants under Rule 5653(c)(4) of the Nasdaq Global Select Market with terms similar to the 2014 Plan (together the “2014 Plans”). At the annual general meeting of shareholders in June 2025, the Company’s shareholders authorized an additional 2,400,000 shares for issuance under the 2014 Plan. As of December 31, 2025, a total of 4,285,461 ordinary shares remain available for issuance under the 2014 Plan. In June 2018, the Company’s shareholders adopted and approved the uniQure N.V. Employee Stock Purchase Plan (as amended, the “ESPP”) allowing the Company to issue up to 150,000 ordinary shares. The ESPP is intended to qualify under Section 423 of the Internal Revenue Code of 1986, as amended. Under the ESPP, employees are eligible to purchase ordinary shares through payroll deductions, subject to any plan limitations. The purchase price of the ordinary shares on each purchase date is equal to the lower of: (i) 85 % of the closing market price on the offering date or (ii) 85 % of the closing market price on the purchase date of each three-month offering period. During the year ended December 31, 2025, nil ordinary shares have been issued in connection with the ESPP (2024: 10,150 ordinary shares and 2023: 19,198 ordinary shares). As of December 31, 2025, a total of 86,712 ordinary shares remain available for issuance under the ESPP plan. 150 ​ Table of Contents 2014 Plans and ESPP ​ Share-based compensation expense recognized by classification included within the Consolidated Statements of Operations and Comprehensive Loss in relation to the 2014 Plans for the periods indicated below was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Cost of contract manufacturing revenues ​ $ — ​ $ 1,035 ​ $ 826 Research and development expenses ​ ​ 7,579 ​ ​ 9,295 ​ ​ 16,881 Selling, general and administrative expenses ​ ​ 10,100 ​ ​ 11,928 ​ ​ 17,386 Total ​ $ 17,679 ​ $ 22,258 ​ $ 35,093 ​ Share-based compensation expense recognized by award type for the 2014 Plans and ESPP was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 6,927 ​ $ 9,178 ​ $ 13,302 Restricted share units ​ ​ 10,709 ​ ​ 11,490 ​ ​ 18,524 Performance share units ​ ​ 14 ​ ​ 1,580 ​ ​ 3,234 ESPP ​ ​ 29 ​ ​ 10 ​ ​ 33 Total ​ $ 17,679 ​ $ 22,258 ​ $ 35,093 ​ As of December 31, 2025, the unrecognized share-based compensation expense related to unvested awards under the 2014 Plans were: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized ​ Weighted average ​ ​ ​ ​ share-based ​ ​ ​ remaining ​ ​ compensation ​ period for ​ ​ expense ​ ​ ​ ​ ​recognition ​ ​ (in thousands) ​ (in years) Award type ​ ​ ​ ​ ​ Share options ​ $ 11,764 ​ 2.50 Restricted share units ​ ​ 20,434 ​ 2.22 Performance share units ​ ​ 83 ​ 0.33 Total ​ $ 32,281 ​ 2.32 ​ The Company satisfies the exercise of share options and vesting of Restricted Share Units (“RSUs”) and Performance Share Units (“PSUs”) through newly issued ordinary shares. ​ Share options Share options are priced on the date of grant and, except for certain grants made to non-executive directors, vest over a period of four years . The first 25 % vests after one year from the initial grant date and the remainder vests in equal quarterly installments over years two, three and four. Certain grants to non-executive directors vest in full after one year . Any options that vest must be exercised by the tenth anniversary of the initial grant date. 151 ​ Table of Contents The following tables summarize option activity under the Company’s 2014 Plans for the year ended December 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ ​ ​ Number of ordinary shares ​ ​ ​ ​ Weighted average exercise price ​ ​ ​ Weighted average remaining contractual life ​ ​ ​ ​ Aggregate intrinsic value ​ ​ ​ ​ ​ ​ ​ in years ​ ​ (in thousands) Outstanding at December 31, 2024 ​ 4,967,160 ​ ​ 19.87 ​ 5.91 ​ $ 19,196 Granted ​ 1,220,410 ​ $ 12.63 ​ ​ ​ ​ ​ Forfeited ​ ( 126,365 ) ​ $ 13.11 ​ ​ ​ ​ ​ Expired ​ ( 834,335 ) ​ $ 29.87 ​ ​ ​ ​ ​ Exercised ​ ( 694,879 ) ​ $ 16.06 ​ ​ ​ ​ ​ Outstanding at December 31, 2025 ​ 4,531,991 ​ $ 17.04 ​ 7.16 ​ ​ 41,816 Thereof, fully vested, and exercisable on December 31, 2025 ​ 2,532,676 ​ $ 21.17 ​ 5.98 ​ ​ 17,574 Thereof, outstanding and expected to vest after December 31, 2025 ​ 1,999,315 ​ $ 11.81 ​ 8.67 ​ ​ 24,242 Outstanding and expected to vest after December 31, 2024 ​ 1,838,603 ​ $ 11.46 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ ​ ​ ​ ​ $ 9.4 ​ ​ ​ ​ ​ ​ ​ ​ ​ Granted to directors and officers during the period (options, grant date fair value $ in millions) ​ 532,410 ​ $ 3.8 ​ ​ ​ ​ ​ Proceeds from option sales during the period (in $ millions) ​ ​ ​ $ 11.1 ​ ​ ​ ​ ​ ​ The following table summarizes information about the weighted average grant-date fair value of options for the years ended December 31, 2025, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Options ​ grant ‑ date fair value Granted, 2025 1,220,410 ​ $ 7.68 Granted, 2024 1,093,080 ​ ​ 3.19 Granted, 2023 1,650,030 ​ ​ 10.57 Vested, 2025 ​ 867,475 ​ ​ 6.69 Forfeited, 2025 ​ ( 126,365 ) ​ ​ 7.71 ​ The following table summarizes information about the weighted average grant-date fair value of options at December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Options ​ grant ‑ date fair value Outstanding and expected to vest, 2025 1,999,315 ​ $ 7.04 Outstanding and expected to vest, 2024 1,838,603 ​ ​ 6.66 ​ The fair value of each option issued is estimated at the respective grant date using the Hull & White option pricing model with the following weighted-average assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 Assumptions ​ ​ ​ ​ ​ ​ Expected volatility ​ 70 % - 80 % ​ 70 % ​ 70 % Expected terms ​ 10 years ​ 10 years ​ 10 years Risk-free interest rate ​ 4.4 % - 4.6 % ​ 3.7 % - 4.3 % ​ 3.7 % - 4.8 % Expected dividend yield ​ 0.0 % ​ 0.0 % ​ 0.0 % ​ 152 ​ Table of Contents The Hull & White option model captures early exercises by assuming that the likelihood of exercises will increase when the share price reaches defined multiples of the strike price. This analysis is performed over the full contractual term. ​ The following table summarizes information about options exercised for the years ended December 31, 2025, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Options exercised ​ ​ ​ ​ ​ ​ ​ during the year ​ Intrinsic value ​ ​ ​ ​ (in thousands) 2025 694,879 ​ $ 19,480 2024 169,898 ​ 248 2023 14,070 ​ 154 ​ RSUs ​ The following table summarizes the RSU activity for the year ended December 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSUs ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2024 ​ 1,659,898 ​ $ 10.71 Granted ​ 1,751,190 ​ $ 13.18 Vested ​ ( 776,882 ) ​ $ 12.04 Forfeited ​ ( 238,786 ) ​ $ 10.04 Non-vested at December 31, 2025 ​ 2,395,420 ​ $ 12.15 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 23.1 Granted to directors and officers during the period (shares, $ in millions) ​ 300,790 ​ $ 3.6 ​ The following table summarizes information about the weighted average grant-date fair value of RSUs granted for the years ended December 31, 2025, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Granted ​ ​ ​ Weighted average ​ ​ during the year ​ grant ‑ date fair value 2025 1,751,190 ​ $ 13.18 2024 1,321,360 ​ ​ 5.57 2023 1,770,025 ​ ​ 17.88 ​ The following table summarizes information about the total fair value of RSUs that vested for the years ended December 31, 2025, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ Total fair value ​ ​ (in thousands) 2025 ​ $ 11,477 2024 ​ 5,603 2023 ​ 13,729 ​ RSUs generally vest over one to three years . RSUs granted to non-executive directors will vest one year from the date of grant. ​ 153 ​ Table of Contents PSUs ​ The following table summarizes the PSU activity for the year ended December 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2024 ​ 150,120 ​ $ 21.65 Vested ​ ( 66,500 ) ​ $ 26.70 Forfeited ​ ( 61,120 ) ​ $ 18.46 Non-vested at December 31, 2025 ​ 22,500 ​ $ 15.40 ​ The Company granted shares to certain employees in 2021 and 2022 that were earned upon the achievement of defined milestones. Earned shares vested upon the latter of a minimum service period of three years , or the achievement of defined milestones, subject to the grantee’s continued employment. In addition, the December 2021 PSUs granted to executives and other members of senior management were subject to the achievement of a minimum total shareholder return relative to the Nasdaq biotechnology index. As of December 31, 2025, there are no remaining milestones to be achieved in relation to the PSUs granted in 2021 and 2022. ​ The Company granted PSUs to certain employees in December 2024. As of December 31, 2025, a percentage of those PSUs were determined probable of being achieved within a defined period in 2026. These PSUs are earned upon the achievement of a certain development milestone, and will vest shortly after the performance goal is determined to be achieved, subject to the grantee’s continued employment. ​ The following table summarizes information about the weighted average grant-date fair value of the PSUs determined as of the grant date for the years ended December 31, 2025, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Granted ​ ​ ​ Weighted average ​ ​ during the year ​ grant ‑ date fair value 2025 — ​ $ — 2024 65,000 ​ $ 15.40 2023 — ​ $ — ​ The following table summarizes information about the total fair value of PSUs that vested during the years ended December 31, 2025, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ Total fair value ​ ​ ​ ​ (in thousands) 2025 ​ $ 803 2024 ​ 319 2023 ​ 1,474 ​ ​ 154 ​ Table of Contents ​ 16. Segment reporting ​ The Company is advancing a pipeline of innovative gene therapies seeking to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company manages the operations related to these research and development activities within one operating segment because they rely on a common set of infrastructure, resources and technology of the products and production processes, types of customers, distribution methods and regulatory environment. ​ The leadership team is identified as the CODM. ​ The CODM allocates resources to research projects and clinical candidates based on scientific data as well as quantitative and qualitative expected risk adjusted returns on investment. The CODM uses segment operating loss to monitor that cash operating losses remain within the approved budget. ​ The Company does not evaluate performance or allocate resources based on segment asset data and therefore such information is not presented. Refer to Note 7 “ Property, plant and equipment, net ” and Note 8 “ Right-of-use asset and lease liabilities ” for geographic information related to long-lived assets. ​ The accounting policies of the operating segment are the same as those described in the summary of significant accounting policies. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Revenue ​ $ 16,098 ​ $ 27,119 ​ $ 15,843 Less: ​ ​ ​ ​ ​ ​ ​ ​ Employee related expenses ​ ( 56,653 ) ​ ( 75,184 ) ​ ( 98,903 ) Laboratory and development expenses ​ ​ ( 69,292 ) ​ ​ ( 47,848 ) ​ ​ ( 44,346 ) Professional fees ​ ​ ( 14,969 ) ​ ​ ( 8,503 ) ​ ​ ( 16,918 ) Facility expenses ​ ​ ( 6,933 ) ​ ​ ( 14,247 ) ​ ​ ( 21,550 ) Consumables ​ ​ ( 3,254 ) ​ ​ ( 9,172 ) ​ ​ ( 19,029 ) Other segment items (a) (b) ​ ​ ( 9,052 ) ​ ​ ( 12,482 ) ​ ​ ( 28,299 ) Segment operating loss ​ ​ ( 144,056 ) ​ ​ ( 140,317 ) ​ ​ ( 213,202 ) Reconciliation ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation and amortization expense ​ ​ ( 14,759 ) ​ ​ ( 12,641 ) ​ ​ ( 11,900 ) Share-based compensation expense ​ ​ ( 17,679 ) ​ ​ ( 22,258 ) ​ ​ ( 35,093 ) Fair value (loss) / gain - contingent consideration ​ ​ ( 6,247 ) ​ ​ 1,817 ​ ​ ( 15,895 ) Fair value gain - liability related to pre-funded warrants ​ ​ 12,405 ​ ​ — ​ ​ ​ Foreign currency gains / (losses), net ​ ​ 26,131 ​ ​ ( 10,507 ) ​ ​ ( 1,691 ) Interest income ​ ​ 16,967 ​ ​ 21,415 ​ ​ 19,562 Interest expense - Royalty Financing Agreement ​ ​ ( 54,099 ) ​ ( 50,865 ) ​ ( 26,934 ) Interest expense - Hercules debt facility ​ ​ ( 6,924 ) ​ ​ ( 12,876 ) ​ ​ ( 14,623 ) Other reconciling items (c) (d) ​ ​ ( 5,079 ) ​ ​ ( 10,895 ) ​ ​ ( 6,781 ) Consolidated loss before income tax expense ​ $ ( 193,340 ) ​ $ ( 237,127 ) ​ $ ( 306,557 ) (a) Other segment items included in segment operating loss include costs related to intellectual property, information technology and insurance offset by income related to payments received from European authorities to subsidize the Company’s research and development in the Netherlands and France. (b) For the year ended December 31, 2023, other segment items include $ 10.0 million related to the upfront consideration paid to Apic Bio for the global licensing agreement for AMT-162. (c) For the year ended December 31, 2024, other reconciling items include costs related to the divestment of the Company’s commercial manufacturing activities and the August 2024 reorganization. (d) For the year ended December 31, 2023, other reconciling items include costs related to the October 2023 reorganization and professional fees related to the Apic Bio transaction. ​ 155 ​ Table of Contents 17. Collaboration arrangements and concentration of credit risk Genezen On June 29, 2024, as part of the Lexington Transaction, uniQure Inc. entered into the CSA and the DMSA with Genezen. As part of the consideration received in relation to the Lexington Transaction, the Company received a convertible promissory note with a nominal amount of $ 12.5 million, bearing interest at 8.0 % per annum and maturing 63 months following the date of issuance. Refer to Note 3 “ Divestiture of commercial manufacturing activities” for further information. As of December 31, 2025 and 2024, the balance of the convertible note receivable was $ 14.6 million and $ 13.7 million, respectively. The Company recorded a balance of prepaid expenses to Genezen in relation to the CSA and DMSA of $ 13.9 million and nil as of December 31, 2025 and 2024, respectively. These balances represent a concentration of credit risk, and the Company’s maximum exposure to loss is the carrying value of these assets. No expected credit loss was recognized during the years ended December 31, 2025 or 2024. ​ CSL Behring collaboration ​ Revenues recorded for the years ended December 31, 2025, 2024 and 2023 were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ ​ 2025 ​ ​ ​ ​ 2024 ​ ​ ​ ​ 2023 ​ ​ (in thousands) License revenue (royalty payments) from CSL Behring ​ $ 15,934 ​ $ 10,133 ​ $ 2,758 Collaboration revenue from CSL Behring ​ ​ 164 ​ 10,872 ​ ​ 2,250 Contract manufacturing revenue from CSL Behring ​ ​ — ​ 6,114 ​ 10,835 Total ​ $ 16,098 ​ $ 27,119 ​ $ 15,843 ​ Collaboration revenue from CSL Behring The Company provides on-demand development services and other services to CSL Behring. These activities are reimbursed at an agreed full-time employee rate, and CSL Behring also reimburses agreed third-party expenses incurred in connection with the performance of these activities. The Company recognized $ 0.2 million of collaboration revenue in the year ended December 31, 2025, compared to $ 10.9 million and $ 2.3 million in the same periods in 2024 and 2023. Contract manufacturing revenue from CSL Behring The DCSA requires the Company to supply HEMGENIX to CSL Behring until such time that these capabilities are transferred to CSL Behring or a contract manufacturing organization designated by CSL Behring. On September 6, 2022, CSL Behring notified the Company of its intent to transfer manufacturing technology related to HEMGENIX in the coming years to a third-party contract manufacturer designated by CSL Behring. The Company generated nil , $ 6.1 million, and $ 10.8 million of contract manufacturing revenue from sales to CSL Behring during the years ended December 31, 2025, 2024 and 2023. The Company incurred nil , $ 17.1 million, and $ 13.6 million of costs in relation to its contract manufacturing activities during the years ended December 2025, 2024 and 2023. Accounts receivable As of December 31, 2025, accounts receivable totaled $ 5.9 million, and related to royalty revenue due from CSL Behring. As of December 31, 2024, accounts receivable totaled $ 5.7 million, and related to collaboration services, contract manufacturing revenue and royalty revenue, due from CSL Behring. ​ 18. Other income ​ Other income during the year ended December 31, 2025 was $ 14.4 million compared to $ 7.9 million and $ 6.1 156 ​ Table of Contents million during the same periods in 2024 and 2023. ​ During the year ended December 31, 2025 the Company recognized $ 6.0 million in income related to a one-time sale of critical reagents to Genezen. There were no sales of critical reagents in the comparative periods in 2024 or 2023. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Sale of critical reagents to Genezen ​ $ 6,000 ​ $ — ​ $ — Research and development grants from Dutch authorities ​ 5,681 ​ 5,602 ​ 5,293 Sublease income ​ 2,101 ​ 1,073 ​ 609 Gain on sale of commercial manufacturing activities ​ ​ — ​ ​ 1,150 ​ ​ — Other ​ 628 ​ 101 ​ 157 Total ​ $ 14,410 ​ $ 7,926 ​ $ 6,059 ​ ​ 19. Other expense ​ Other expense during the year ended December 31, 2025 was $ 8.0 million compared to $ 4.6 million and $ 1.7 million during the same periods in 2024 and 2023, respectively. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Supply of HEMGENIX® to CSL Behring ​ $ 6,251 ​ $ 3,215 ​ $ — Sublease expense ​ 1,791 ​ 1,358 ​ 900 Fair value loss related to equity stake in VectorY B.V. ​ ​ — ​ ​ — ​ ​ 790 Total ​ $ 8,042 ​ $ 4,573 ​ $ 1,690 ​ In the years ended December 31, 2025 and 2024, the Company recognized $ 6.3 million and $ 3.2 million, respectively ( nil in the period ended December 31, 2023) in Other expense related to the purchase of HEMGENIX from Genezen, net of income from the sales of HEMGENIX to CSL Behring, amortization of the intangible asset for the favorable supply terms under the CSA and credits from the release of liabilities related to expected net losses associated with the minimum purchase commitments under the CSA. ​ 20. Income taxes ​ a. Income tax expense ​ Due to the uncertainty surrounding the realization of favorable tax attributes in future tax returns, a valuation allowance is recorded against the Company’s net deferred tax assets in the Netherlands, and a partial valuation allowance against the Company’s net deferred tax assets in France. ​ There are no significant unrecognized tax benefits as of December 31, 2025 and 2024. ​ For the years ended December 31, 2025, 2024 and 2023, loss before income tax expense consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Domestic - Netherlands ​ $ ( 174,507 ) ​ $ ( 215,251 ) ​ $ ( 282,530 ) Foreign - U.S. ​ ( 4,470 ) ​ ( 1,133 ) ​ ( 6,903 ) Foreign - Other ​ ​ ( 14,363 ) ​ ​ ( 20,743 ) ​ ​ ( 17,124 ) Total ​ $ ( 193,340 ) ​ $ ( 237,127 ) ​ $ ( 306,557 ) ​ ​ 157 ​ Table of Contents The income tax expense for the years ended December 31, 2025, 2024 and 2023, consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Current tax expense ​ ​ ​ ​ ​ ​ ​ ​ ​ Domestic - Netherlands ​ $ ( 3,907 ) ​ $ — ​ $ — Other ​ ​ ( 136 ) ​ ​ ( 145 ) ​ ​ ( 110 ) Total current income tax expense ​ $ ( 4,043 ) ​ $ ( 145 ) ​ $ ( 110 ) Deferred tax expense ​ ​ ​ ​ ​ ​ Domestic - Netherlands ​ $ ( 466 ) ​ $ — ​ $ — Other ​ ​ ( 1,122 ) ​ ​ ( 2,284 ) ​ ​ ( 1,811 ) Total deferred tax expense ​ ​ ( 1,588 ) ​ ​ ( 2,284 ) ​ ​ ( 1,811 ) Total income tax expense ​ $ ( 5,631 ) ​ $ ( 2,429 ) ​ $ ( 1,921 ) ​ b. Income taxes paid ​ The income taxes paid during the years ended December 31, 2025, 2024 and 2023 were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Domestic - Netherlands ​ $ 7,403 ​ $ — ​ $ — Foreign ​ ​ 139 ​ ​ 21 ​ ​ 12 Total ​ $ 7,542 ​ $ 21 ​ $ 12 ​ Since 2023, the Company has been engaged with the Dutch tax authorities regarding the Dutch corporate income tax treatment of the $ 375.0 million upfront payment received in exchange for the rights to the lowest royalty tier on CSL Behring’s worldwide net sales of HEMGENIX. In September 2025, the Dutch tax authorities communicated their position that, for Dutch corporate income tax purposes, the upfront payment should be treated as taxable income in 2023. In response, the Company revised its Dutch corporate income tax filing position to reflect the upfront payment as taxable income in 2023 (net of directly attributable expenses), together with a revision of a previously filed tax position, which resulted in a taxable profit of EUR 12.9 million ($ 14.6 million) for 2023, instead of the previous taxable loss for that year. ​ During 2025, the Company made a provisional payment of EUR 6.4 million ($ 7.4 million) in respect of the revised 2023 filing position. Subsequently, in conjunction with finalizing its positions, the Company also amended its 2021 Dutch corporate income tax filing position, which reduced the Company’s estimated Dutch corporate income tax related to 2023 to EUR 3.3 million ($ 3.9 million). ​ c. Tax benefit recognized in other comprehensive loss related to defined benefit pension plan liability ​ The reconciliation of the amount of income tax (loss) / benefit related to the defined benefit pension plan liability recognized in other comprehensive loss for the years ended December 31, 2025, 2024 and 2023, is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) Unrecognized gain / (loss) related to defined benefit pension plan liability ​ $ 887 ​ $ 384 ​ $ ( 2,553 ) Deferred tax (expense) / benefit ​ ​ ( 116 ) ​ ​ ( 57 ) ​ ​ 417 Unrecognized gain / (loss) related to defined benefit pension plan liability, net of tax ​ $ 771 ​ $ 327 ​ $ ( 2,136 ) ​ ​ 158 ​ Table of Contents d. Tax rate reconciliation ​ The reconciliation of the amount of income tax expense that would result from applying the domestic Dutch statutory income tax rate to the Company’s reported amount of loss before income tax expense for the years ended December 31, 2025, 2024 and 2023, is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2025 ​ 2024 ​ 2023 ​ ​ ​ ​ Amount ​ ​ ​ Percent ​ ​ ​ Amount ​ ​ ​ Percent ​ ​ ​ Amount ​ ​ ​ Percent ​ ​ (in thousands) ​ ​ ​ ​ (in thousands) ​ ​ ​ ​ (in thousands) ​ ​ ​ Domestic statutory tax rate - Netherlands ​ $ 49,882 ​ ​ 25.8 % ​ $ 61,179 ​ ​ 25.8 % ​ $ 79,092 ​ ​ 25.8 % Foreign tax effects (difference in tax rates between the Netherlands and foreign jurisdictions) ​ ​ ( 160 ) ​ ​ ( 0.1 %) ​ ​ ( 149 ) ​ ​ ( 0.1 %) ​ ​ ( 124 ) ​ ​ ( 0.0 %) Domestic ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Changes in valuation allowance ​ ​ ( 42,095 ) ​ ​ ( 21.8 %) ​ ​ ( 53,745 ) ​ ​ ( 22.7 %) ​ ​ ( 64,319 ) ​ ​ ( 21.0 %) Non-deductible items ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Fair value changes ​ ​ ( 4,687 ) ​ ​ ( 2.4 %) ​ ​ 471 ​ ​ 0.2 % ​ ​ ( 4,132 ) ​ ​ ( 1.3 %) Other ​ ​ ( 1,705 ) ​ ​ ( 0.9 %) ​ ​ ( 2,417 ) ​ ​ ( 1.0 %) ​ ​ ( 4,442 ) ​ ​ ( 1.4 %) Foreign ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Changes in valuation allowance ​ ​ ( 3,518 ) ​ ​ ( 1.8 %) ​ ​ ( 3,805 ) ​ ​ ( 1.6 %) ​ ​ ( 2,685 ) ​ ​ ( 0.9 %) Non-deductible items ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Share-based payment awards ​ ​ ( 2,746 ) ​ ​ ( 1.4 %) ​ ​ ( 3,083 ) ​ ​ ( 1.3 %) ​ ​ ( 5,332 ) ​ ​ ( 1.7 %) Other ​ ​ 44 ​ ​ 0.0 % ​ ​ ( 655 ) ​ ​ ( 0.3 %) ​ ​ ( 119 ) ​ ​ ( 0.0 %) Other adjustments ​ ​ ( 646 ) ​ ​ ( 0.3 %) ​ ​ ( 225 ) ​ ​ ( 0.1 %) ​ ​ 140 ​ ​ 0.0 % Total tax provision and effective tax rate ​ $ ( 5,631 ) ​ ​ ( 2.9 %) ​ $ ( 2,429 ) ​ ​ ( 1.0 %) ​ $ ( 1,921 ) ​ ​ ( 0.6 %) ​ e. Significant components of deferred taxes ​ The tax effects of temporary differences and carryforwards that give rise to significant portions of deferred tax assets and deferred tax liabilities as of December 31, 2025 and 2024 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2025 ​ 2024 ​ ​ (in thousands) Deferred tax assets: ​ ​ ​ ​ Net operating loss carryforwards ​ $ 162,869 ​ $ 178,421 Liability from royalty financing agreement ​ ​ 123,042 ​ ​ 19,476 Intangibles ​ ​ 1,866 ​ ​ 4,702 Operating lease liabilities ​ ​ 3,588 ​ ​ 3,846 Accrued expenses and other current liabilities ​ ​ 3,034 ​ ​ 3,069 Interest carryforwards ​ ​ — ​ ​ 2,956 Property, plant and equipment ​ 1,007 ​ 365 Defined benefit pension plan liability ​ ​ 207 ​ ​ 260 Total deferred tax assets ​ $ 295,613 ​ $ 213,095 Less valuation allowance ​ ( 271,429 ) ​ ( 191,864 ) Deferred tax assets, net of valuation allowance ​ $ 24,184 ​ $ 21,231 Acquired IPR&D intangible asset ​ ​ ( 16,238 ) ​ ​ ( 14,341 ) Operating lease right-of-use assets ​ ​ ( 3,564 ) ​ ​ ( 3,864 ) Other current assets and receivables ​ ​ ( 3,308 ) ​ ​ ( 48 ) Property, plant and equipment ​ ​ ( 387 ) ​ ​ ( 165 ) Deferred tax liability ​ $ ( 23,497 ) ​ $ ( 18,418 ) Net deferred tax asset ​ $ 687 ​ $ 2,813 ​ 159 ​ Table of Contents Changes in the valuation allowance during the years ended December 31, 2025, 2024 and 2023 were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands) January 1, ​ $ 191,864 ​ $ 145,191 ​ $ 74,547 Changes recorded in the statement of operations ​ ​ 45,613 ​ ​ 57,550 ​ ​ 67,004 Changes recorded in equity ​ ​ 6,525 ​ ​ — ​ ​ — Other changes including currency translation adjustments ​ 27,427 ​ ( 10,877 ) ​ 3,640 December 31, ​ $ 271,429 ​ $ 191,864 ​ $ 145,191 ​ The valuation allowance of $ 271.4 million as of December 31,2025 is primarily related to EUR 221.9 million ($ 260.7 million) of deferred tax assets in the Netherlands resulting from net operating loss carryforwards of EUR 118.4 million ($ 139.1 million), and a liability from the Royalty Financing Agreement of EUR 104.7 million ($ 123.0 million). Netherlands As of December 31, 2025, the total amount of net operating losses carried forward under the Dutch tax regime was EUR 458.9 million ($ 539.2 million), following the alignment of the Dutch corporate income tax treatment of the Royalty Financing Agreement in 2025, which consumed EUR 13.9 million ($ 15.7 million) of such net operating losses carried forward to 2025, and resulted in the recognition of a deferred tax asset related to the Liability from royalty financing agreement. As of December 31, 2024, the total amount of net operating losses carried forward was EUR 593.6 million ($ 616.5 million). The Company has historically recorded a full valuation allowance. The Company evaluates all positive and negative evidence in assessing the need for a full valuation allowance. Management considers reversing taxable temporary differences, projected future taxable income and tax-planning strategies in making this assessment. The Company concluded that as of December 31, 2025, and December 31, 2024 it is more likely than not that the remaining deferred tax assets will not be realized. The Company’s Dutch net operating tax losses carried forward relate to 2019, 2022, 2024 and 2025. A portion of the valuation allowance for deferred tax assets recorded as of December 31, 2025 relates to follow-on offering costs incurred in 2019 and 2025. During the year ended December 31, 2025, the Company released $ 0.5 million of the valuation allowance related to 2019 and recorded a deferred tax expense as a result of adjusting the 2023 and 2021 Dutch corporate income tax filing positions. Any subsequently recognized tax benefits will be credited directly to Additional paid-in capital. As of December 31, 2025, that amount was EUR 8.4 million ($ 9.9 million) and EUR 3.0 million ($ 3.2 million) as of December 31, 2024. The Dutch corporate tax rate is 25.8 % from 2022 onwards. Net operating loss carryforwards subject to a limit of offsetting taxable profit in excess of EUR 1.0 million to 50% of the taxable profit can be carried forward indefinitely. The fiscal periods from 2021 onwards are still open for inspection by the Dutch tax authorities. United States of America The federal corporate tax rate in the U.S. is 21.0 %. In addition, the Company is subject to state income taxes resulting in a combined tax rate of 27.3 % for its U.S. operation. As of December 31, 2025, an estimated $ 20.1 million of net operating losses remain to be carried forward. These net operating losses carried forward will expire in 2036 and 2037 except for $ 0.7 million which may be carried forward indefinitely with a deduction limited to 80% of taxable income in a given year. The Company’s U.S. operations have been generating taxable income since 2018 with the exception of 2022. The Company expects to continue to generate taxable income in the U.S. during the foreseeable future. ​ ​ 160 ​ Table of Contents Under the provision of the Internal Revenue Code, the U.S. net operating losses carried forward may become subject to an annual limitation in the event of certain cumulative exchange in the ownership interest of significant shareholders over a three-year period, in excess of 50%, as defined under Section 382 and 383 of the Internal Revenue Code. This could limit the amount of tax attributes that can be utilized annually to offset future taxable income or tax liabilities. The amount of the annual limitation is determined based on the value of the Company immediately prior to the ownership change. Subsequent ownership changes may further affect the limitation. The fiscal periods from 2022 are still open for inspection by the IRS. To the extent the Company has tax attribute carryforwards, the tax years in which the attribute was generated may still be adjusted upon examination by the IRS or Massachusetts Department of Revenue to the extent utilized in a future period. The Company is currently not under examination by the IRS for any tax years. France The French corporate tax rate for fiscal year 2025 was 25.0 %. In addition, the Company is subject to a surcharge of 3.3 % of the 25.0 % standard corporate tax rate resulting in a combined rate of 25.8 %. The Company’s French operations have incurred losses since incorporation and are expected to continue incurring tax losses for the foreseeable future. The French operations as of December 31, 2025 have an estimated EUR 59.8 million ($ 70.3 million) of net operating losses EUR 48.9 million ($ 50.8 million) as of December 31, 2024) that are available for carry forward indefinitely. The Company recorded a partial valuation allowance during the years ended December 31, 2025, 2024, and 2023. The Company evaluates all positive and negative evidence including future income from reversing taxable temporary differences (particularly from reversing the deferred tax liability related to the acquired IPR&D intangible asset), projected future taxable income subject to the loss limitation rules applicable in France and tax-planning strategies in making this assessment. ​ 21. Basic and diluted loss per ordinary share ​ Basic net loss per ordinary share is computed by dividing net loss for the period by the weighted average number of ordinary shares outstanding during the period. Diluted earnings per ordinary share are calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. As the Company incurred a loss in all years presented, all potentially dilutive ordinary shares for these years would have an anti-dilutive effect, if converted, and thus have been excluded from the computation of basic and diluted loss per ordinary share. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 ​ ​ (in thousands, except share amounts) Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss attributable to ordinary shares ​ $ ( 198,971 ) ​ $ ( 239,556 ) ​ $ ( 308,478 ) Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-average number of ordinary shares outstanding - basic and diluted ​ ​ 57,502,068 ​ ​ 48,649,129 ​ ​ 47,670,986 ​ 161 ​ Table of Contents The following table presents ordinary share equivalents that were excluded from the calculation of diluted loss per ordinary share for all years presented, as the effect of their inclusion would have been anti-dilutive: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ ​ ​ 2025 ​ ​ ​ 2024 ​ ​ ​ 2023 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans ​ $ 4,531,991 ​ $ 4,967,160 ​ ​ 4,974,030 Non-vested RSUs and PSUs ​ ​ 2,417,920 ​ ​ 1,810,018 ​ ​ 2,486,919 Pre-Funded Warrants ​ ​ 526,316 ​ ​ — ​ ​ — ESPP ​ ​ 13,936 ​ ​ — ​ ​ 3,640 Total anti-dilutive ordinary share equivalents ​ ​ 7,490,163 ​ ​ 6,777,178 ​ ​ 7,464,589 ​ The anti-dilutive ordinary shares are presented without giving effect to the application of the treasury method or exercise prices that exceeded the price of the Company’s ordinary shares as of December 31, 2025, December 31, 2024 and December 31, 2023. ​ ​ ​ 22. Commitments and contingencies ​ In the course of its business, the Company enters as a licensee into contracts with other parties regarding the development and marketing of its pipeline products. Among other payment obligations, the Company is obligated to pay royalties to the licensors based on future sales levels and milestone payments whenever specified development, regulatory and commercial milestones are met. As both future sales levels and the timing and achievement of milestones are uncertain, the financial effect of these agreements cannot be reliably estimated. The Company also has obligations to make future payments that become due and payable upon the collection of milestone payments from CSL Behring. The achievement and timing of these milestones is not fixed or determinable. Relevant commitments and contingencies are further discussed in other sections of this form 10-K, such as, Note 3 “ Divestiture of manufacturing facility ” and Note 17 “ Collaboration arrangements and concentration of credit risk ”, amongst others. ​ Legal Proceedings ​ On February 10, 2026, a class action complaint captioned Christopher Scocco v. uniQure N.V., et al. , Case No. 1:26-cv-01124, was filed against the Company, certain of the Company’s executive officers and another party in the United States District Court for the Southern District of New York. The complaint purports to assert claims pursuant to Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended, and Rule 10b-5 promulgated thereunder, on behalf of a putative class of investors who purchased or otherwise acquired our ordinary shares between September 24, 2025 and October 31, 2025. Plaintiff seeks to recover damages allegedly caused by purported false and misleading misstatements and omissions with respect to the Company’s Phase I/II study of AMT-130 and the timing of the potential BLA filing for AMT-130. The Company intends to vigorously defend against the claims in this action. ​ At each reporting date, the Company evaluates whether or not a potential loss amount or a potential range of loss is probable and reasonably estimable under the provisions of the authoritative guidance that addresses accounting for contingencies. At this time, the Company is unable to predict the outcome of the class action litigation or reasonably estimate a range of possible losses. ​ 23. Related party transaction ​ None. ​ 24. Subsequent events ​ None. ​ ​ ​ 162 ​ Table of Contents EXHIBIT INDEX ​ Exhibit No. ​ ​ ​ Description 2.1† ​ Sale and Purchase Agreement, executed June 21, 2021, by and between uniQure N.V. and Corlieve Therapeutics SAS (incorporated by reference to Exhibit 2.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 3.1 ​ Amended Articles of Association of the Company (incorporated by reference to Exhibit 3.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 4.1* ​ Description of the Registrant’s Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934. 4.2 ​ Form of Pre-Funded Warrant (incorporated by reference to Exhibit 4.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on September 29, 2025). 10.1 t ​ 2014 Share Incentive Plan (incorporated by reference to Exhibit 4.3 of the Company’s Registration Statement on Form S-8 (file no. 333-225629) filed with the SEC on June 14, 2018). 10.2t ​ Amended and Restated 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on November 17, 2023). 10.3t ​ Amended and Restated 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on June 13, 2025). 10.4t ​ Amended and Restated 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on June 20, 2024). 10.5t ​ Form of Share Option Agreement, effective December 8, 2021, under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.65 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.6t ​ Form of Restricted Stock Unit Award, effective December 8, 2021, under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.66 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.7t+ ​ Form of Performance Stock Unit Award, effective December 8, 2021 under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.67 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.8t ​ Employee Share Purchase Plan (incorporated by reference to Exhibit 4.2 of the Company’s Registration Statement on Form S-8 (file no. 333-225629) filed with the SEC on June 14, 2018). 10.9t ​ Amended and Restated Employee Share Purchase Plan (incorporated by reference to Exhibit 10.2 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended March 31, 2025 filed with the SEC on May 9, 2025). 1 0.10t ​ Amended and Restated Employment Agreement between uniQure, Inc. and Matthew Kapusta, dated April 15, 2025 (incorporated by reference to Exhibit 10.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended March 31, 2025 filed with the SEC on May 9, 2025). 10.11t ​ Amended and Restated Employment Agreement, effective June 15, 2021, by and between uniQure biopharma B.V. and Christian Klemt (incorporated by reference to Exhibit 10.3 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 10.12t ​ Employment Agreement dated May 22, 2023 between uniQure, Inc. and Jeannette Potts (incorporated by reference to Exhibit 10.77 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2023 (file no. 001-36294) filed with the SEC on February 28, 2024). 163 ​ Table of Contents 10.13t ​ Employment Agreement dated June 26, 2023 between uniQure Switzerland GmbH (formerly Corlieve Therapeutics AG) and Walid Abi-Saab (incorporated by reference to Exhibit 10.1 6 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 (file no. 001-36294) filed with the SEC on February 27, 2025). 10.14 ​ Lease relating to 113 Hartwell Avenue, Lexington, Massachusetts, dated as of July 24, 2013, by and between uniQure Inc. and King 113 Hartwell LLC (incorporated by reference to Exhibit 10.28 of the Company’s Registration Statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.15 ​ First Amendment Lease relating to 113 Hartwell Avenue, Lexington, Massachusetts, dated as of July 24, 2013, by and between the Company and King113 Hartwell LLC (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on November 15, 2018). 10.16 ​ Second Amendment Lease relating to 113 Hartwell Avenue, Lexington Massachusetts, dated as of June 17, 2019, by and between the Company and King 113 Hartwell LLC (incorporated by reference to Exhibit 10.42 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2019 filed with the SEC on July 29, 2019). 10.17 ​ Landlord Consent to Assignment and Assumption of Lease and Third Amendment to Lease, dated June 28, 2024, by and among Hartwell Innovation Campus, LLC, uniQure, Inc. and Genezen MA, Inc. (incorporated by reference to Exhibit 10.3 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ending June 30, 2024 filed with the SEC on August 1, 2024). 10.18 ​ Assignment and Assumption of Lease, dated July 22, 2024, by and between uniQure, Inc. and Genezen MA, Inc. (incorporated by reference to Exhibit 10.4 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ending June 30, 2024 filed with the SEC on August 1, 2024). 10.19 ​ Lease relating to Paasheuvelweg 25, dated as of March 7, 2016, by and between 52 IFH GmbH & Co. KG and uniQure biopharma B.V. (incorporated by reference to Exhibit 10.36 of the Company’s Annual Report on Form 10-K (file no. 001-36294) for the year ended December 31, 2016 filed with the SEC on March 15, 2017). 10.20 ​ Lease Agreement relating to 91 Hartwell Avenue, Lexington, Massachusetts, dated as of February 1, 2022, by and between uniQure Inc. and NRL 91 Hartwell LLC (incorporated by reference to Exhibit 10.70 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.21 ​ Lease Agreement relating to Peter Merian-Weg 4, 4052 Basel, Switzerland, dated as of November 1, 2023, by and between uniQure Switzerland GmbH (formerly Corlieve Therapeutics AG) and Stiftung Sympany (incorporated by reference to Exhibit 10.24 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 (file no. 001-36294) filed with the SEC on February 27, 2025). 10.22* + Addendum No. 1 to the Lease Agreement relating to Peter Merian-Weg 4, 4052 Basel, Switzerland, dated as of January 6, 2026, by and between uniQure Switzerland GmbH and Stiftung Sympany. 10.23 ​ Business Acquisition Agreement, dated as of February 16, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding N.V., the Company and the other Parties listed therein (incorporated by reference to Exhibit 10.29 of the Company’s Registration Statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.24 ​ Deed of Assignment of Certain Assets and Liabilities of Amsterdam Molecular Therapeutics (AMT) Holding N.V., dated as of April 5, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding B.V., Amsterdam Molecular Therapeutics (AMT) Holding IP B.V. and Amsterdam Molecular Therapeutics (AMT) Holding N.V. (incorporated by reference to Exhibit 10.30 of the Company's Registration Statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 164 ​ Table of Contents 10.25 ​ Agreement for Transfer of Certain Assets and Liabilities of Amsterdam Molecular Therapeutics (AMT) Holding N.V., dated as of February 16, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding B.V., Amsterdam Molecular Therapeutics (AMT) Holding IP B.V. and Amsterdam Molecular Therapeutics (AMT) Holding N.V. (incorporated by reference to Exhibit 10.31 of the Company’s Registration Statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.26† ​ Assignment and License Agreement dated April 17, 2017 between Professor Paolo Simioni and uniQure biopharma B.V. (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on October 19, 2017). 10.27† ​ Commercialization and License Agreement by and between uniQure biopharma B.V. and CSL Behring LLC dated June 24, 2020 (incorporated by reference to Exhibit 10.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2020 filed with the SEC on July 30, 2020). 10.28† ​ Third Amended and Restated Loan and Security Agreement as of December 15, 2021, by and among uniQure biopharma B.V., uniQure Inc., uniQure IP B.V., the Company and Hercules Capital Inc (incorporated by reference to Exhibit 10.68 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.29 + ​ Amendment No. 3 to Third Amended and Restated Loan and Security Agreement, dated of September 22, 2025, by and among uniQure biopharma, B.V., uniQure, Inc., uniQure IP B.V., the Company and Hercules Capital, Inc. (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on September 24, 2025). 10.30† ​ Royalty Purchase Agreement, dated May 12, 2023, by and between uniQure biopharma B.V. and HemB SPV, L.P. (incorporated by reference to Exhibit 10.2 of the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2023 (file no. 001-36294) filed with the SEC on August 1, 2023). 10.31† ​ Asset Purchase Agreement, by and among uniQure, Inc., uniQure biopharma B.V., Genezen Holdings Inc. and Genezen MA, Inc., dated as of June 29, 2024 (incorporated by reference to Exhibit 10.1 of the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2024 (file no. 001-36294) filed with the SEC on August 1, 2024). 14.1* ​ Code of Ethics . 19.1 ​ Insider Trading Policy (incorporated by reference to Exhibit 19.1 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 (file no. 001-36294) filed with the SEC on February 27, 2025). 21.1* ​ Subsidiaries of the Company. 23.1* ​ Consent of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 24.1* ​ Power of Attorney (incorporated by reference to the signature page of this Annual Report on Form 10-K). 31.1* ​ Rule 13a-14(a)/15d-14(a) Certification of Chief Executive Officer. 31.2* ​ Rule 13a-14(a)/15d-14(a) Certification of Chief Financial Officer. 32.1** ​ Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 97.1 ​ Compensation Clawback Policy (incorporated by reference to Exhibit 97.1 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2023 (file no. 001-36294) filed with the SEC on February 28, 2024). 101* ​ The following materials from the Company’s Annual Report on Form 10-K for the year ended December 31, 2025, formatted in Inline XBRL (eXtensible Business Reporting Language): (i) Consolidated Balance Sheets, (ii) Consolidated Statements of Operations and Comprehensive Income (Loss), (iii) Consolidated Statements of Shareholders’ Equity / (Deficit), (iv) Consolidated Statements of Cash Flows and (v) Notes to Consolidated Financial Statements. 104* ​ The cover page from the Company’s Annual Report on Form 10-K for the year ended December 31, 2025 has been formatted in Inline XBRL. 165 ​ Table of Contents ​ † Confidential treatment requested as to certain portions, which portions have been omitted and filed separately with the Securities and Exchange Commission ​ + Portions of this exhibit have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K. ​ * Filed herewith. ​ ** Furnished herewith. ​ t Indicates a management contract or compensatory plan or arrangement. ​ ​ 166 ​ Table of Contents SIGNATURES ​ Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. ​ ​ ​ ​ ​ UNIQURE N.V. ​ ​ ​ Date: March 2, 2026 By: /s/ MATTHEW KAPUSTA ​ ​ Matthew Kapusta ​ ​ Chief Executive Officer (Principal Executive Officer) ​ ​ ​ Date: March 2, 2026 By: /s/ CHRISTIAN KLEMT ​ ​ Christian Klemt ​ ​ Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer) ​ POWER OF ATTORNEY ​ KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Matthew Kapusta and Christian Klemt, jointly and severally, his or her attorney-in-fact, with the power of substitution, for him or her in any and all capacities, to sign any amendments to this Annual Report on Form 10-K and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming all that each of said attorneys-in-fact, or his or her substitute or substitutes, may do or cause to be done by virtue hereof. ​ Pursuant to the requirements of the Securities Exchange Act of 1934, this Annual Report on Form 10-K has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated. ​ Signatures ​ ​ ​ Title ​ ​ ​ Date ​ ​ ​ ​ ​ /s/ MATTHEW KAPUSTA ​ Chief Executive Officer and Director (Principal Executive Officer) ​ March 2, 2026 Matthew Kapusta ​ ​ ​ ​ ​ ​ ​ /s/ CHRISTIAN KLEMT ​ Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer) ​ March 2, 2026 Christian Klemt ​ ​ ​ ​ ​ ​ ​ /s/ MADHAVAN BALACHANDRAN ​ Director ​ March 2, 2026 Madhavan Balachandran ​ ​ ​ ​ ​ ​ ​ /s/ ROBERT GUT ​ Director ​ March 2, 2026 Robert Gut ​ ​ ​ ​ ​ ​ ​ /s/ RACHELLE JACQUES ​ Director ​ March 2, 2026 Rachelle Jacques ​ ​ ​ ​ ​ ​ ​ /s/ JACK KAYE ​ Director ​ March 2, 2026 Jack Kaye ​ ​ ​ ​ ​ ​ ​ /s/ DAVID MEEK ​ Director ​ March 2, 2026 David Meek ​ ​ ​ ​ ​ ​ ​ /s/ LEONARD POST ​ Director ​ March 2, 2026 Leonard Post ​ ​ ​ ​ ​ ​ ​ /s/ JEREMY P. SPRINGHORN ​ Director ​ March 2, 2026 Jeremy P. Springhorn ​ ​ ​ ​ ​ ​ 167 ​