uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 139,994 ​ $ 80,240 Current investment securities ​ ​ 446,556 ​ ​ 542,301 Accounts receivable ​ ​ 3,562 ​ ​ 5,863 Prepaid expenses ​ ​ 16,589 ​ ​ 20,506 Other current assets and receivables ​ ​ 9,043 ​ ​ 7,076 Total current assets ​ ​ 615,744 ​ ​ 655,986 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net ​ ​ 12,014 ​ ​ 13,800 Other investments ​ ​ 30,150 ​ ​ 30,237 Operating lease right-of-use assets ​ ​ 12,261 ​ ​ 12,525 Intangible assets, net ​ ​ 69,990 ​ ​ 72,790 Goodwill ​ ​ 24,811 ​ ​ 25,355 Deferred tax assets, net ​ ​ 8,194 ​ ​ 8,654 Other non-current assets ​ ​ 5,542 ​ ​ 5,561 Total non-current assets ​ ​ 162,962 ​ ​ 168,922 Total assets ​ $ 778,706 ​ $ 824,908 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 4,399 ​ $ 5,170 Accrued expenses and other current liabilities ​ ​ 43,201 ​ ​ 41,292 Liability related to pre-funded warrants ​ ​ 8,605 ​ ​ 12,595 Current portion of operating lease liabilities ​ ​ 2,992 ​ ​ 3,862 Total current liabilities ​ ​ 59,197 ​ ​ 62,919 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 49,942 ​ ​ 49,699 Liability from royalty financing agreement ​ ​ 482,334 ​ ​ 473,199 Operating lease liabilities, net of current portion ​ ​ 10,388 ​ ​ 9,832 Contingent consideration ​ ​ 17,029 ​ ​ 18,736 Deferred tax liability, net ​ ​ 7,796 ​ ​ 7,967 Other non-current liabilities, net of current portion ​ ​ 2,677 ​ ​ 3,655 Total non-current liabilities ​ ​ 570,166 ​ ​ 563,088 Total liabilities ​ ​ 629,363 ​ ​ 626,007 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized at March 31, 2026, and December 31, 2025, and 63,033,249 and 62,336,717 shares issued and outstanding at March 31, 2026, and December 31, 2025, respectively. ​ ​ 3,728 ​ ​ 3,688 Additional paid-in-capital ​ ​ 1,587,971 ​ ​ 1,582,371 Accumulated other comprehensive loss ​ ​ ( 59,885 ) ​ ​ ( 58,222 ) Accumulated deficit ​ ​ ( 1,382,471 ) ​ ​ ( 1,328,936 ) Total shareholders' equity ​ ​ 149,343 ​ ​ 198,901 Total liabilities and shareholders' equity ​ $ 778,706 ​ $ 824,908 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ 2 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands, except share and per share amounts) License revenues ​ $ 3,562 ​ $ 1,567 Total revenues ​ ​ 3,562 ​ ​ 1,567 Operating expenses: ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 219 ) ​ ​ ( 197 ) Research and development expenses ​ ​ ( 29,176 ) ​ ​ ( 36,140 ) Selling, general and administrative expenses ​ ​ ( 20,068 ) ​ ​ ( 10,908 ) Total operating expenses ​ ​ ( 49,463 ) ​ ​ ( 47,245 ) Other income ​ ​ 1,632 ​ ​ 8,306 Other expense ​ ​ ( 1,451 ) ​ ​ ( 1,959 ) Loss from operations ​ ​ ( 45,720 ) ​ ​ ( 39,331 ) Interest income ​ ​ 5,229 ​ ​ 4,127 Interest expense ​ ​ ( 14,031 ) ​ ​ ( 15,109 ) Foreign currency (losses) / gains, net ​ ​ ( 2,294 ) ​ ​ 7,172 Other non-operating gains, net ​ ​ 3,769 ​ ​ — Loss before income tax expense ​ $ ( 53,047 ) ​ $ ( 43,141 ) Income tax expense ​ ​ ( 488 ) ​ ​ ( 496 ) Net loss ​ $ ( 53,535 ) ​ $ ( 43,637 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ Foreign currency translation losses, net ​ ​ ( 1,663 ) ​ ​ ( 1,005 ) Total comprehensive loss ​ $ ( 55,198 ) ​ $ ( 44,642 ) Loss per ordinary share - basic and diluted ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 0.85 ) ​ $ ( 0.82 ) Weighted average shares - basic and diluted ​ ​ 62,742,847 ​ ​ 53,110,580 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements . ​ 3 Table of Contents ​ uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY FOR THE THREE MONTHS ENDED MARCH 31, 2026 AND 2025 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ ​ ​ ​ No. of shares ​ ​ ​ Amount ​ ​ ​ capital ​ ​ ​ loss ​ ​ ​ deficit ​ ​ ​ equity ​ ​ (in thousands, except share and per share amounts) Balance at December 31, 2024 ​ 48,988,087 ​ $ 2,945 ​ $ 1,173,068 ​ $ ( 52,800 ) ​ $ ( 1,129,965 ) ​ $ ( 6,752 ) Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 43,637 ) ​ ​ ( 43,637 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 1,005 ) ​ ​ — ​ ​ ( 1,005 ) Follow-on public offering ​ 5,073,529 ​ ​ 261 ​ ​ 80,250 ​ ​ — ​ ​ — ​ ​ 80,511 Exercises of share options ​ 15,928 ​ ​ 1 ​ ​ 158 ​ ​ — ​ ​ — ​ ​ 159 Restricted and performance share units distributed during the period ​ 620,935 ​ ​ 33 ​ ​ ( 33 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 4,410 ​ ​ — ​ ​ — ​ ​ 4,410 Balance at March 31, 2025 ​ 54,698,479 ​ $ 3,240 ​ $ 1,257,853 ​ $ ( 53,805 ) ​ $ ( 1,173,602 ) ​ $ 33,686 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2025 ​ 62,336,717 ​ $ 3,688 ​ $ 1,582,371 ​ $ ( 58,222 ) ​ $ ( 1,328,936 ) ​ $ 198,901 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 53,535 ) ​ ​ ( 53,535 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 1,663 ) ​ ​ — ​ ​ ( 1,663 ) Exercises of share options ​ 25,308 ​ ​ 1 ​ ​ 384 ​ ​ — ​ ​ — ​ ​ 385 Restricted share units distributed during the period ​ 657,285 ​ ​ 38 ​ ​ ( 38 ) ​ ​ — ​ ​ — ​ ​ — Issuance of ordinary shares relating to employee stock purchase plan ​ 13,939 ​ ​ 1 ​ ​ 164 ​ ​ — ​ ​ — ​ ​ 165 Share-based compensation expense ​ — ​ ​ — ​ ​ 5,090 ​ ​ — ​ ​ — ​ ​ 5,090 Balance at March 31, 2026 ​ 63,033,249 ​ $ 3,728 ​ $ 1,587,971 ​ $ ( 59,885 ) ​ $ ( 1,382,471 ) ​ $ 149,343 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements . ​ 4 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 53,535 ) ​ $ ( 43,637 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization ​ ​ 2,956 ​ ​ 4,527 Amortization of discount on investment securities ​ ​ ( 4,335 ) ​ ​ ( 2,117 ) Share-based compensation expense ​ ​ 5,090 ​ ​ 4,410 Royalty financing agreement interest expense, net of interest paid ​ ​ 7,173 ​ ​ 8,358 Deferred tax expense ​ ​ 458 ​ ​ 496 Changes in fair value of contingent consideration ​ ​ ( 1,338 ) ​ ​ 1,216 Changes in fair value of liability related to pre-funded warrants ​ ​ ( 3,769 ) ​ ​ — Unrealized foreign exchange losses / (gains), net ​ ​ 2,178 ​ ​ ( 7,105 ) Other items, net ​ ​ ( 242 ) ​ ​ ( 3,971 ) Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ 3,780 ​ ​ ( 2,979 ) Accounts payable ​ ​ ( 557 ) ​ ​ ( 2,093 ) Accrued expenses, other liabilities, and operating leases ​ ​ 3,898 ​ ​ ( 1,205 ) Net cash used in operating activities ​ ​ ( 38,243 ) ​ ​ ( 44,100 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Proceeds on maturity of debt securities ​ ​ 98,700 ​ ​ 85,000 Investment in debt securities ​ ​ — ​ ​ ( 64,775 ) Purchases of property, plant, and equipment ​ ​ ( 140 ) ​ ​ ( 126 ) Net cash generated from investing activities ​ ​ 98,560 ​ ​ 20,099 Cash flows from financing activities ​ ​ ​ ​ ​ ​ Proceeds from follow-on public offering of ordinary shares, net of issuance costs ​ ​ — ​ ​ 80,511 Proceeds from issuance of ordinary shares related to employee stock options and purchase plans ​ ​ 550 ​ ​ 159 Net cash generated from financing activities ​ ​ 550 ​ ​ 80,670 Currency effect on cash, cash equivalents and restricted cash ​ ​ ( 1,132 ) ​ ​ 1,660 Net increase in cash, cash equivalents and restricted cash ​ ​ 59,735 ​ ​ 58,329 Cash, cash equivalents and restricted cash at the beginning of period ​ ​ 81,801 ​ ​ 160,329 Cash, cash equivalents and restricted cash at the end of period ​ $ 141,536 ​ $ 218,658 Cash and cash equivalents ​ $ 139,994 ​ $ 217,229 Restricted cash related to leasehold and other deposits ​ ​ 1,542 ​ ​ 1,429 Total cash, cash equivalents and restricted cash ​ $ 141,536 ​ $ 218,658 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 6,720 ) ​ $ ( 6,491 ) ​ The accompanying notes are an integral part of these unaudited consolidated financial statements . ​ ​ 5 Table of Contents uniQure N.V. ​ NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) ​ 1 General business information ​ uniQure N.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, its registered office is located at Paasheuvelweg 25a, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000. ​ 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 these unaudited consolidated financial statements in compliance with generally accepted accounting principles in the United States (“U.S. GAAP”) and applicable rules and regulations of the United States Securities and Exchange Commission (the “SEC”) regarding interim financial reporting. 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 Updates of the Financial Accounting Standards Board. ​ The unaudited 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. ​ 2.2 Unaudited interim financial information ​ The interim financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the financial position, results of operations and changes in financial position for the period presented. ​ Certain information and footnote disclosures normally included in annual financial statements prepared in accordance with U.S. GAAP have been omitted. The results of operations for the three months ended March 31, 2026 are not necessarily indicative of the results to be expected for the full year ending December 31, 2026, or for any other future year or interim period. The accompanying financial statements should be read in conjunction with the audited financial statements and the related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025 filed by the Company with the SEC on March 2, 2026 (the “Annual Report”). ​ 6 Table of Contents 2.3 Use of estimates ​ The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent liabilities at the date of the financial statements and reported amounts of revenues, expenses and tax related items during the reporting period. Actual results could differ from those estimates. ​ 2.4 Accounting policies ​ The principal accounting policies applied in the preparation of these unaudited consolidated financial statements are described in the Company’s audited financial statements as of and for the year ended December 31, 2025, and the notes thereto, which are included in the Annual Report . There have been no material changes in the Company’s significant accounting policies during the three months ended March 31, 2026. ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the three months ended March 31, 2026, as compared to the recent accounting pronouncements described in Note 2.3.29 of the Annual Report , which could be expected to materially impact the Company’s unaudited consolidated financial statements. ​ 3 Current investment securities ​ The following tables summarize the Company’s investments in government debt securities as of March 31, 2026 and December 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At March 31, 2026 ​ ​ ​ ​ Amortized cost ​ ​ ​ Gross unrealized holding gains ​ ​ ​ Gross unrealized holding losses ​ ​ ​ Estimated fair value ​ ​ (in thousands) Current investments securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 446,556 ​ $ 295 ​ $ — ​ $ 446,851 Total ​ $ 446,556 ​ $ 295 ​ $ — ​ $ 446,851 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2025 ​ ​ ​ ​ Amortized cost ​ ​ ​ Gross unrealized holding gains ​ ​ ​ Gross unrealized holding losses ​ ​ ​ Estimated fair value ​ ​ (in thousands) Current investments securities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 542,301 ​ $ 308 ​ $ — ​ $ 542,609 Total ​ $ 542,301 ​ $ 308 ​ $ — ​ $ 542,609 ​ 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 (€, or EUR) denominated, respectively. Investment securities with original maturities of 90 days or less when purchased are presented within cash and cash equivalents and measured at amortized cost. Inputs to the fair value of the investments are considered Level 2 inputs. ​ As of March 31, 2026 and December 31, 2025, no expected credit loss was identified with respect to the investment securities. ​ 7 Table of Contents 4 Fair value measurement ​ The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ASC 820 , Fair Value Measurement requires disclosure of the 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. ​ 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 Unaudited 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 unaudited Consolidated Balance Sheets. Investment securities are measured at amortized cost. ​ 8 Table of Contents The following table sets forth the Company’s assets and liabilities that are required to be measured at fair value on a recurring basis as of March 31, 2026 and December 31, 2025 : ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Quoted prices in active markets (Level 1) ​ ​ Significant other observable inputs (Level 2) ​ ​ Significant unobservable inputs (Level 3) ​ ​ Total ​ ​ Classification in Unaudited Consolidated Balance Sheets ​ ​ ​ (in thousands) ​ ​ Balance at December 31, 2025 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 80,240 ​ $ — ​ $ — ​ $ 80,240 ​ Cash and cash equivalents Restricted cash ​ ​ 1,561 ​ ​ — ​ ​ — ​ ​ 1,561 ​ Other non-current assets Total assets ​ $ 81,801 ​ $ — ​ $ — ​ $ 81,801 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Liability related to pre-funded warrants ​ ​ — ​ ​ 12,595 ​ ​ — ​ ​ 12,595 ​ Liability related to pre-funded warrants Contingent consideration ​ ​ — ​ ​ — ​ ​ 18,736 ​ ​ 18,736 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 638 ​ ​ 638 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ 12,595 ​ $ 19,374 ​ $ 31,969 ​ ​ Balance at March 31, 2026 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 139,994 ​ $ — ​ $ — ​ $ 139,994 ​ Cash and cash equivalents Restricted cash ​ ​ 1,542 ​ ​ — ​ ​ — ​ ​ 1,542 ​ Other non-current assets Total assets ​ $ 141,536 ​ $ — ​ $ — ​ $ 141,536 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Liability related to pre-funded warrants ​ ​ — ​ ​ 8,605 ​ ​ — ​ ​ 8,605 ​ Liability related to pre-funded warrants Contingent consideration ​ ​ — ​ ​ — ​ ​ 17,029 ​ ​ 17,029 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 580 ​ ​ 580 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ 8,605 ​ $ 17,609 ​ $ 26,214 ​ ​ ​ a) Contingent consideration ​ The Company is required to pay up to EUR 143.1 million (or $ 164.5 million based on the foreign exchange rate on March 31, 2026) to the former shareholders of uniQure France SAS (formerly Corlieve Therapeutics SAS) upon the achievement of the remaining contractually defined milestones related to the development of AMT-260 in connection with the Company’s acquisition of uniQure France SAS. ​ The fair value of the contingent consideration as of March 31, 2026 was EUR 14.8 million ($ 17.0 million) (December 31, 2025: EUR 15.9 million ($ 18.7 million)) using discount rates of approximately 11.5 % to 11.8 % (December 31, 2025: 11.8 %). ​ If, as of March 31, 2026, 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 47.8 million ($ 55.0 million). If, as of March 31, 2026, the Company had assumed that it would discontinue development of the AMT-260 program, then the contingent consideration would have been released to income. ​ The following table presents the changes in fair value of the contingent consideration (presented within non-current liabilities) between December 31, 2025 and March 31, 2026: ​ ​ ​ ​ ​ ​ ​ ​ Amount of ​ ​ contingent ​ ​ consideration ​ ​ (in thousands) Balance at December 31, 2025 ​ $ 18,736 Unrealized change in fair value (presented within Research and development expenses) ​ ​ ( 1,338 ) Currency translation effects ​ ​ ( 369 ) Balance at March 31, 2026 ​ $ 17,029 ​ 9 Table of Contents The Company classified the total contingent consideration liability as non-current as of March 31, 2026 and December 31, 2025. The classification of the contingent consideration within the Company’s Unaudited Consolidated Balance Sheets between current and non-current liabilities is based upon the Company’s best estimate of the timing of settlement of the remaining relevant milestones. ​ b) 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 (“Pre-Funded Warrant(s)”). 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 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. ​ ​ ​ ​ ​ ​ ​ Liability related ​ ​ to pre-funded ​ ​ warrants ​ ​ (in thousands) Balance at December 31, 2025 ​ $ 12,595 Unrealized change in fair value (presented within Other non-operating gains, net) ​ ​ ( 3,769 ) Currency translation effects ​ ​ ( 221 ) Balance at March 31, 2026 ​ $ 8,605 ​ ​ ​ 5 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Accruals for goods received from and services provided by vendors-not yet billed ​ $ 23,493 ​ ​ 20,490 Personnel-related accruals and liabilities ​ ​ 10,126 ​ $ 9,941 Current portion of firm purchase commitment liability (refer to Note 13, "Commitments and contingencies" ) ​ ​ 5,796 ​ ​ 5,102 Liability owed to the Purchaser pursuant to the Royalty Financing Agreement (refer to Note 7, " Royalty Financing Agreement ") ​ ​ 3,562 ​ ​ 5,523 Other current liabilities ​ ​ 224 ​ ​ 236 Total ​ $ 43,201 ​ $ 41,292 ​ ​ ​ 6 Long-term debt ​ The total principal outstanding as of March 31, 2026 under the Company's amended venture debt loan facility with Hercules Capital, Inc. (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 $ 50.3 million as of March 31, 2026, compared to $ 50.1 million as of December 31, 2025, and is recorded net of discount and debt issuance costs. ​ The foreign currency loss on the loan facility in the three months ended March 31, 2026 was $ 1.1 million, compared to a foreign currency gain of $ 2.1 million during the same period in 2025. Interest expense during the three months ended March 31, 2026 was $ 1.4 million, compared to $ 1.8 million during the same period in 2025. ​ During the three months ended March 31, 2026, there were no material changes to the terms, available borrowing tranches, covenants, or collateral arrangements of the 2025 Amended Facility as described in Note 11, “Long-term debt” to the consolidated financial statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025. As of March 31, 2026, the Company was in compliance with all applicable covenants under the facility. 10 Table of Contents 7 Royalty Financing Agreement ​ During the three months ended March 31, 2026, there were no material changes to the terms of the royalty purchase agreement entered into in May 2023 (the “Royalty Financing Agreement”) with HemB SPV, L.P. (the “Purchaser”), as described in Note 12, “ Royalty Financing Agreement ” within the consolidated financial statements included in the Company’s Annual Report for the year ended December 31, 2025. ​ The following table presents the changes in the liability from royalty financing agreement for the period from December 31, 2025 to March 31, 2026: ​ ​ ​ ​ ​ ​ ​ ​ ​ Amount of liability ​ ​ (in thousands) Balance as of December 31, 2025 (includes $ 5.5 million presented as "Accrued expenses and other current liabilities") ​ ​ 478,722 Royalty payments to the Purchaser ​ ​ ( 5,523 ) Interest expense for the period ​ ​ 12,621 Balance as of March 31, 2026 (includes $ 3.6 million presented as "Accrued expenses and other current liabilities") ​ $ 485,820 ​ The Company records the debt at amortized cost using the effective interest rate method based on projected cash flows. As of March 31, 2026, the effective interest rate is expected to be within a range of 10.5 % to 12.0 % per annum (March 31, 2025: 12.0 % to 13.5 %). Interest expense recorded in connection with the agreement was $ 12.6 million and $ 13.3 million for the three months ended March 31, 2026 and 2025, respectively. ​ ​ ​ ​ ​ ​ ​ 8 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”). As of March 31, 2026, a total of 2,571,395 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. ​ 2014 Plans and ESPP ​ Share-based compensation expense recognized by classification included in the Unaudited Consolidated Statements of Operations and Comprehensive Loss in relation to the 2014 Plans and the ESPP for the periods indicated below was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Research and development expenses ​ ​ 1,977 ​ ​ 2,463 Selling, general and administrative expenses ​ ​ 3,113 ​ ​ 1,947 Total ​ $ 5,090 ​ $ 4,410 ​ 11 Table of Contents Share-based compensation expense recognized by award type for the 2014 Plans as well as the ESPP was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ Share options ​ $ 1,807 ​ $ 1,637 Restricted share units ​ ​ 3,206 ​ ​ 2,213 Performance share units ​ ​ 62 ​ ​ 560 ESPP ​ ​ 15 ​ ​ — Total ​ $ 5,090 ​ $ 4,410 ​ As of March 31, 2026, 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 ​ $ 14,881 ​ 2.88 Restricted share units ​ ​ 27,279 ​ 2.40 Performance share units ​ ​ 21 ​ 0.08 Total ​ $ 42,181 ​ 2.57 ​ 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 % of each grant vests one year after 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. The following table summarizes option activity under the 2014 Plans for the three months ended March 31, 2026: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ ​ ​ Number of ordinary shares ​ ​ ​ ​ Weighted average exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2025 ​ 4,531,991 ​ ​ 17.04 Granted ​ 771,900 ​ $ 9.53 Forfeited ​ — ​ $ — Expired ​ ( 11,466 ) ​ $ 37.00 Exercised ​ ( 25,308 ) ​ $ 15.24 Outstanding at March 31, 2026 ​ 5,267,117 ​ $ 15.90 Thereof, fully vested, and exercisable on March 31, 2026 ​ 2,825,796 ​ $ 20.06 Thereof, outstanding and expected to vest after March 31, 2026 ​ 2,441,321 ​ $ 11.09 Outstanding and expected to vest after December 31, 2025 ​ 1,999,315 ​ $ 11.81 ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ ​ ​ ​ ​ $ 4.9 ​ 12 Table of Contents 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: ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 Assumptions ​ ​ ​ ​ Expected volatility ​ 95.0 % ​ 80.0 % Expected terms ​ 10 years ​ 10 years Risk-free interest rate ​ 4.2 % - 4.3 % ​ 4.4 % Expected dividend yield ​ 0.0 % ​ 0.0 % ​ RSUs ​ The following table summarizes the RSU activity for the three months ended March 31, 2026: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSUs ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2025 ​ 2,395,420 ​ $ 12.15 Granted ​ 997,100 ​ $ 10.77 Vested ​ ( 657,285 ) ​ $ 11.33 Forfeited ​ ( 43,468 ) ​ $ 15.72 Non-vested at March 31, 2026 ​ 2,691,767 ​ $ 11.78 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 10.7 ​ RSUs are measured at grant date based on the market price of the Company’s ordinary shares and, except for certain grants made to non-executive directors, vest over a three-year period. RSUs granted to non-executive directors vest one year after the date of grant. ​ PSUs ​ The Company granted PSUs to certain employees in 2024 and 2026, that, with respect to the 2024 PSUs, will be earned upon the Board of Directors’ assessment of the level of achievement of agreed upon performance targets, and, with respect to the 2026 PSUs, will be earned upon management’s assessment of the level of achievement of agreed upon performance targets, subject, in each case, to the grantee’s continued employment. The fair value of PSUs granted in 2024 and 2026 was determined on the grant date by reference to the market price of the Company’s ordinary shares. ​ The Company recognizes the compensation cost related to these grants to the extent it considers achievement of the milestones to be probable. As of March 31, 2026, the PSUs granted in 2026 were assessed as not probable of achieving the requisite performance conditions in accordance with ASC 718, Compensation-Stock Compensation ; therefore, no stock-based compensation expense has been recognized. ​ The following table summarizes the PSU activity for the three months ended March 31, 2026: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2025 ​ 22,500 ​ $ 15.40 Granted ​ — ​ $ — Vested ​ — ​ $ — Forfeited ​ — ​ $ — Non-vested at March 31, 2026 ​ 22,500 ​ $ 15.40 ​ 13 Table of Contents ESPP ​ During the three months ended March 31, 2026, 13,939 ordinary shares were issued under the ESPP compared to nil ordinary shares issued during the same period in 2025. As of March 31, 2026, 72,773 ordinary shares remain available for issuance under the ESPP compared to a total of 86,712 ordinary shares as of March 31, 2025. ​ ​ 9 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 Chief Operating Decision Maker (“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 accounting policies of the operating segment are the same as those described in the summary of significant accounting policies. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Revenue ​ $ 3,562 ​ $ 1,567 Less: ​ ​ ​ ​ ​ Employee related expenses ​ ( 16,786 ) ​ ( 14,216 ) Laboratory and development expenses ​ ​ ( 14,761 ) ​ ​ ( 15,967 ) Professional fees ​ ​ ( 4,507 ) ​ ​ ( 2,057 ) Information technology system costs ​ ​ ( 1,659 ) ​ ​ ( 1,001 ) Facility expenses ​ ​ ( 1,547 ) ​ ​ ( 1,667 ) Other segment items (1) ​ ​ ( 3,513 ) ​ ​ ( 969 ) Segment operating loss ​ ​ ( 39,211 ) ​ ​ ( 34,310 ) Reconciliation ​ ​ ​ ​ ​ ​ Depreciation and amortization expense ​ ​ ( 2,956 ) ​ ​ ( 4,527 ) Share-based compensation expense ​ ​ ( 5,090 ) ​ ​ ( 4,410 ) Fair value gain / (loss) - contingent consideration ​ ​ 1,338 ​ ​ ( 1,216 ) Fair value gain - liability related to pre-funded warrants ​ ​ 3,769 ​ ​ — Foreign currency (losses) / gains, net ​ ​ ( 2,294 ) ​ ​ 7,172 Interest income ​ ​ 5,229 ​ ​ 4,127 Interest expense - Royalty Financing Agreement ​ ​ ( 12,621 ) ​ ( 13,309 ) Interest expense - Hercules loan facility ​ ​ ( 1,410 ) ​ ​ ( 1,800 ) Other reconciling items ​ ​ 199 ​ ​ 5,132 Consolidated loss before income tax expense ​ $ ( 53,047 ) ​ $ ( 43,141 ) ​ (1) Other segment items included in segment operating loss include costs related to intellectual property and insurance offset by income related to payments received from European authorities to subsidize the Company’s research and development in the Netherlands. ​ ​ 14 Table of Contents 10 Other investments and concentration of credit risk ​ The following table summarizes the Company’s other investments as of March 31, 2026 and December 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Carrying amount of investments valued under measurement alternative ​ $ 15,280 ​ $ 15,615 Convertible note receivable ​ ​ 14,870 ​ ​ 14,622 Total ​ $ 30,150 ​ $ 30,237 ​ The Company did not recognize any upward adjustments, downward adjustments, or impairments relating to investments carried under the measurement alternative during the three months ended March 31, 2026, and 2025. Genezen In 2024, as part of the Company’s divestment of its commercial manufacturing operations to Genezen Holdings Inc. and its subsidiary Genezen MA, Inc. (together “Genezen”), the Company entered into a commercial supply agreement (the “Genezen CSA”), as well as a development and other manufacturing agreement, with Genezen. The Company recorded a balance of prepaid expenses of $ 12.3 million and $ 13.9 million as of March 31, 2026 and December 31, 2025, respectively, for services that the Company expects to receive from Genezen. In addition, as of March 31, 2026, the Company holds a convertible note receivable of $ 14.9 million which is due in September 2029 and for which Genezen is the counterparty (December 31, 2025: $ 14.6 million). 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 losses were recognized during the three months ended March 31, 2026 or 2025. ​ CSL Behring ​ As of March 31, 2026 and December 31, 2025, accounts receivable from CSL Behring LLC (“CSL Behring”) totaled $ 3.6 million and $ 5.9 million, respectively, in each case related to royalty revenue. ​ ​ ​ 11 Income taxes ​ The Company recorded a deferred tax expense of $ 0.5 million related to its U.S. operations during the three months ended March 31, 2026 ($ 0.5 million for the three months ended March 31, 2025). ​ The effective income tax rate of 0.9 % during the three months ended March 31, 2026 (three months ended March 31, 2025: 1.1 %) is substantially lower than the enacted rate of 25.8 % in the Netherlands as the Company recorded a valuation allowance against its net deferred tax assets in the Netherlands and a partial valuation allowance against its net deferred tax assets in France. ​ ​ ​ 12 Basic and diluted loss per share ​ Diluted loss per ordinary share is 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 the three months ended March 31, 2026 and March 31, 2025, all potentially dilutive ordinary shares would have an antidilutive effect, if converted, and thus have been excluded from the computation of diluted loss per share for the three months ended March 31, 2026 and March 31, 2025. The ordinary shares are presented without giving effect to the application of the treasury method or exercise prices that would be above the share price as of March 31, 2026 and March 31, 2025, respectively. ​ ​ ​ 15 Table of Contents The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans ​ $ 5,267,117 ​ $ 5,283,396 Non-vested RSUs and PSUs ​ ​ 2,714,267 ​ ​ 2,242,926 Pre-Funded Warrants ​ ​ 526,316 ​ ​ — ESPP ​ ​ 13,936 ​ ​ — Total anti-dilutive ordinary share equivalents ​ ​ 8,521,636 ​ ​ 7,526,322 ​ ​ 13 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. ​ As of March 31, 2026, the remaining minimum purchase commitments in connection with the Genezen CSA amount to $ 16.2 million, with $ 13.3 million to be paid within the next 12 months. As of March 31, 2026, CSL Behring’s minimum purchase commitments to the Company over the next 12 months, in connection with the development and commercial supply agreement between the Company and CSL Behring (the “CSL Behring CSA”), amount to $ 16.4 million, of which $ 16.2 million relates to such minimum purchase commitments to Genezen. In April 2026, the Company entered into agreements with Genezen and CSL Behring to terminate the Genezen CSA and the CSL Behring CSA. Refer to Note 14, “ Subsequent events” . 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 its 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 the Company’s ordinary shares between September 24, 2025 and October 31, 2025. Plaintiff seeks to recover damages allegedly caused by purported false and misleading statements 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. ​ ​ ​ ​ ​ ​ ​ 16 Table of Contents 14 Subsequent events ​ Termination agreements with CSL Behring and Genezen ​ Since the Company’s July 2024 divestiture of its commercial manufacturing activities to Genezen, the Company had been sourcing etranacogene dezaparvovec-drlb (“HEMGENIX ® ”) under the Genezen CSA. The Company entered into the Genezen CSA to enable it to meet its obligations to supply HEMGENIX ® in accordance with the June 2020 commercialization and license agreement with CSL Behring (the “CSL Behring Agreement”) (refer to Note 10, “ Other Investments and concentration of credit risk ,” and Note 13, “ Commitments and contingencies ”) until such time that the HEMGENIX ® manufacturing technology had been transferred to CSL Behring or a contract manufacturing organization designated by CSL Behring. The Company, since July 2024, had served as an agent in the sale of HEMGENIX ® to CSL Behring as title to HEMGENIX ® drug product supply had been directly passing from Genezen to CSL Behring. In April 2026, the Company entered into agreements with CSL Behring and Genezen that provide for i) the termination of its obligation to supply HEMGENIX ® and any minimum purchase commitments under the Genezen CSA, once the contractually specified batches have been supplied to CSL Behring, which the Company expects to occur in mid-2026, and ii) the designation of Genezen as CSL Behring’s contract manufacturing organization. In addition, the CSL Behring Agreement was amended to terminate certain manufacturing-related terms associated with both the CSL Behring CSA and the Genezen CSA, as well as the Company’s development support that CSL Behring could request from time to time with respect to HEMGENIX ® . All other terms of the CSL Behring Agreement remain in full force and effect. ​ The Company expects that by the time the contractually specified batches have been supplied to CSL Behring, it will i) have fully amortized the carrying amount of the intangible asset recorded with respect to the favorable supply terms under the Genezen CSA of $ 7.3 million as of March 31, 2026, and ii) have fully released the firm purchase commitment liability with a March 31, 2026 carrying amount of $ 5.8 million. ​ 17 Table of Contents