uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 413,027 ​ $ 80,240 Current investment securities ​ ​ 397,308 ​ ​ 542,301 Accounts receivable ​ ​ 5,778 ​ ​ 5,863 Prepaid expenses ​ ​ 10,245 ​ ​ 20,506 Other current assets and receivables ​ ​ 7,911 ​ ​ 7,076 Total current assets ​ ​ 834,269 ​ ​ 655,986 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net ​ ​ 11,376 ​ ​ 13,800 Other investments ​ ​ 30,267 ​ ​ 30,237 Operating lease right-of-use assets ​ ​ 11,606 ​ ​ 12,525 Intangible assets, net ​ ​ 62,101 ​ ​ 72,790 Goodwill ​ ​ 24,587 ​ ​ 25,355 Deferred tax assets, net ​ ​ 6,362 ​ ​ 8,654 Other non-current assets ​ ​ 4,535 ​ ​ 5,561 Total non-current assets ​ ​ 150,834 ​ ​ 168,922 Total assets ​ $ 985,103 ​ $ 824,908 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 4,979 ​ $ 5,170 Accrued expenses and other current liabilities ​ ​ 51,133 ​ ​ 41,292 Liability related to pre-funded warrants ​ ​ 24,242 ​ ​ 12,595 Current portion of operating lease liabilities ​ ​ 2,991 ​ ​ 3,862 Total current liabilities ​ ​ 83,345 ​ ​ 62,919 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 50,147 ​ ​ 49,699 Liability from royalty financing agreement ​ ​ 489,333 ​ ​ 473,199 Operating lease liabilities, net of current portion ​ ​ 9,696 ​ ​ 9,832 Contingent consideration ​ ​ 18,113 ​ ​ 18,736 Deferred tax liability, net ​ ​ 7,726 ​ ​ 7,967 Other non-current liabilities, net of current portion ​ ​ 2,693 ​ ​ 3,655 Total non-current liabilities ​ ​ 577,708 ​ ​ 563,088 Total liabilities ​ ​ 661,053 ​ ​ 626,007 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 100,000,000 shares authorized at June 30, 2026, and 80,000,000 at December 31, 2025, and 69,334,839 and 62,336,717 shares issued and outstanding at June 30, 2026, and December 31, 2025, respectively. ​ ​ 4,086 ​ ​ 3,688 Additional paid-in capital ​ ​ 1,841,745 ​ ​ 1,582,371 Accumulated other comprehensive loss ​ ​ ( 58,251 ) ​ ​ ( 58,222 ) Accumulated deficit ​ ​ ( 1,463,530 ) ​ ​ ( 1,328,936 ) Total shareholders' equity ​ ​ 324,050 ​ ​ 198,901 Total liabilities and shareholders' equity ​ $ 985,103 ​ $ 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 June 30, ​ Six months ended June 30, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands, except share and per share amounts) ​ (in thousands, except share and per share amounts) License revenues ​ $ 5,841 ​ $ 5,262 ​ $ 9,403 ​ $ 6,829 Total revenues ​ ​ 5,841 ​ ​ 5,262 ​ ​ 9,403 ​ ​ 6,829 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 350 ) ​ ​ ( 656 ) ​ ​ ( 569 ) ​ ​ ( 853 ) Research and development expenses ​ ​ ( 33,964 ) ​ ​ ( 35,383 ) ​ ​ ( 63,140 ) ​ ​ ( 71,523 ) Selling, general and administrative expenses ​ ​ ( 17,367 ) ​ ​ ( 13,500 ) ​ ​ ( 37,435 ) ​ ​ ( 24,408 ) Total operating expenses ​ ​ ( 51,681 ) ​ ​ ( 49,539 ) ​ ​ ( 101,144 ) ​ ​ ( 96,784 ) Other income ​ ​ 1,598 ​ ​ 2,597 ​ ​ 3,230 ​ ​ 10,903 Other expense ​ ​ ( 7,961 ) ​ ​ ( 2,185 ) ​ ​ ( 9,412 ) ​ ​ ( 4,144 ) Loss from operations ​ ​ ( 52,203 ) ​ ​ ( 43,865 ) ​ ​ ( 97,923 ) ​ ​ ( 83,196 ) Interest income ​ ​ 5,051 ​ ​ 3,524 ​ ​ 10,280 ​ ​ 7,651 Interest expense ​ ​ ( 14,366 ) ​ ​ ( 15,591 ) ​ ​ ( 28,397 ) ​ ​ ( 30,700 ) Foreign currency (losses) / gains, net ​ ​ ( 1,730 ) ​ ​ 18,638 ​ ​ ( 4,024 ) ​ ​ 25,810 Other non-operating (losses), net ​ ​ ( 15,970 ) ​ ​ — ​ ​ ( 12,201 ) ​ ​ — Loss before income tax expense ​ $ ( 79,218 ) ​ $ ( 37,294 ) ​ $ ( 132,265 ) ​ $ ( 80,435 ) Income tax expense ​ ​ ( 1,841 ) ​ ​ ( 425 ) ​ ​ ( 2,329 ) ​ ​ ( 921 ) Net loss ​ $ ( 81,059 ) ​ $ ( 37,719 ) ​ $ ( 134,594 ) ​ $ ( 81,356 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation gains / (losses), net ​ ​ 1,634 ​ ​ ( 5,098 ) ​ ​ ( 29 ) ​ ​ ( 6,103 ) Total comprehensive loss ​ $ ( 79,425 ) ​ $ ( 42,817 ) ​ $ ( 134,623 ) ​ $ ( 87,459 ) Loss per ordinary share - basic and diluted ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 1.22 ) ​ $ ( 0.69 ) ​ $ ( 2.09 ) ​ $ ( 1.49 ) Weighted average shares - basic and diluted ​ ​ 66,243,879 ​ ​ 54,807,967 ​ ​ 64,503,035 ​ ​ 54,540,423 ​ 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 / (DEFICIT) FOR THE THREE MONTHS ENDED JUNE 30, 2026 AND 2025 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ ​ ​ ​ No. of shares ​ ​ ​ Amount ​ ​ ​ capital ​ ​ ​ gain / (loss) ​ ​ ​ deficit ​ ​ ​ equity / (deficit) ​ ​ (in thousands, except share and per share amounts) Balance at March 31, 2025 ​ 54,698,479 ​ $ 3,240 ​ $ 1,257,853 ​ $ ( 53,805 ) ​ $ ( 1,173,602 ) ​ $ 33,686 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 37,719 ) ​ ​ ( 37,719 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 5,098 ) ​ ​ — ​ ​ ( 5,098 ) Exercise of share options ​ 5,312 ​ ​ — ​ ​ 44 ​ ​ — ​ ​ — ​ ​ 44 Restricted share units distributed during the period ​ 161,882 ​ ​ 10 ​ ​ ( 10 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 5,084 ​ ​ — ​ ​ — ​ ​ 5,084 Balance at June 30, 2025 ​ 54,865,673 ​ $ 3,250 ​ $ 1,262,971 ​ $ ( 58,903 ) ​ $ ( 1,211,321 ) ​ $ ( 4,003 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at March 31, 2026 ​ 63,033,249 ​ $ 3,728 ​ $ 1,587,971 ​ $ ( 59,885 ) ​ $ ( 1,382,471 ) ​ $ 149,343 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 81,059 ) ​ ​ ( 81,059 ) Other comprehensive gain, net ​ — ​ ​ — ​ ​ — ​ ​ 1,634 ​ ​ — ​ ​ 1,634 Follow-on public offering ​ 5,686,813 ​ ​ 323 ​ ​ 242,359 ​ ​ — ​ ​ — ​ ​ 242,681 Exercises of share options ​ 385,541 ​ ​ 23 ​ ​ 6,412 ​ ​ — ​ ​ — ​ ​ 6,435 Restricted share units distributed during the period ​ 229,236 ​ ​ 13 ​ ​ ( 13 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 5,016 ​ ​ — ​ ​ — ​ ​ 5,016 Balance at June 30, 2026 ​ 69,334,839 ​ $ 4,086 ​ $ 1,841,745 ​ $ ( 58,251 ) ​ $ ( 1,463,530 ) ​ $ 324,050 ​ ​ 4 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY / (DEFICIT) FOR THE SIX MONTHS ENDED JUNE 30, 2026 AND 2025 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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, 2024 ​ 48,988,087 ​ $ 2,945 ​ $ 1,173,068 ​ $ ( 52,800 ) ​ $ ( 1,129,965 ) ​ $ ( 6,752 ) Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 81,356 ) ​ ​ ( 81,356 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 6,103 ) ​ ​ — ​ ​ ( 6,103 ) Follow-on public offering ​ 5,073,529 ​ ​ 261 ​ ​ 80,250 ​ ​ — ​ ​ — ​ ​ 80,511 Exercises of share options ​ 21,240 ​ ​ 1 ​ ​ 202 ​ ​ — ​ ​ — ​ ​ 203 Restricted and performance share units distributed during the period ​ 782,817 ​ ​ 43 ​ ​ ( 43 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 9,494 ​ ​ — ​ ​ — ​ ​ 9,494 Balance at June 30, 2025 ​ 54,865,673 ​ $ 3,250 ​ $ 1,262,971 ​ $ ( 58,903 ) ​ $ ( 1,211,321 ) ​ $ ( 4,003 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2025 ​ 62,336,717 ​ $ 3,688 ​ $ 1,582,371 ​ $ ( 58,222 ) ​ $ ( 1,328,936 ) ​ $ 198,901 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 134,594 ) ​ ​ ( 134,594 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 29 ) ​ ​ — ​ ​ ( 29 ) Follow-on public offering ​ 5,686,813 ​ ​ 323 ​ ​ 242,359 ​ ​ — ​ ​ — ​ ​ 242,681 Exercises of share options ​ 410,849 ​ ​ 24 ​ ​ 6,796 ​ ​ — ​ ​ — ​ ​ 6,820 Restricted share units distributed during the period ​ 886,521 ​ ​ 51 ​ ​ ( 51 ) ​ ​ — ​ ​ — ​ ​ — Issuance of ordinary shares relating to employee stock purchase plan ​ 13,939 ​ ​ 1 ​ ​ 164 ​ ​ — ​ ​ — ​ ​ 165 Share-based compensation expense ​ — ​ ​ — ​ ​ 10,106 ​ ​ — ​ ​ — ​ ​ 10,106 Balance at June 30, 2026 ​ 69,334,839 ​ $ 4,086 ​ $ 1,841,745 ​ $ ( 58,251 ) ​ $ ( 1,463,530 ) ​ $ 324,050 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements . ​ ​ 5 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Six months ended June 30, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 134,594 ) ​ $ ( 81,356 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization ​ ​ 7,863 ​ ​ 8,157 Amortization of discount on investment securities ​ ​ ( 7,907 ) ​ ​ ( 4,163 ) Share-based compensation expense ​ ​ 10,106 ​ ​ 9,494 Royalty financing agreement interest expense, net of interest paid ​ ​ 17,384 ​ ​ 20,626 Deferred tax expense ​ ​ 2,329 ​ ​ 921 Changes in fair value of contingent consideration ​ ​ ( 82 ) ​ ​ 3,470 Changes in fair value of liability related to pre-funded warrants ​ ​ 12,201 ​ ​ — Unrealized foreign exchange losses / (gains), net ​ ​ 8,329 ​ ​ ( 25,163 ) Other items, net ​ ​ ( 2,426 ) ​ ​ ( 3,651 ) Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ 8,846 ​ ​ ( 6,761 ) Accounts payable ​ ​ 68 ​ ​ ( 2,297 ) Accrued expenses, other liabilities, and operating leases ​ ​ 11,064 ​ ​ ( 3,272 ) Net cash used in operating activities ​ ​ ( 66,819 ) ​ ​ ( 83,995 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Proceeds on maturity of debt securities ​ ​ 384,981 ​ ​ 213,763 Investments in debt securities ​ ​ ( 232,550 ) ​ ​ ( 120,205 ) Purchases of property, plant, and equipment ​ ​ ( 612 ) ​ ​ ( 386 ) Net cash generated from investing activities ​ ​ 151,819 ​ ​ 93,172 Cash flows from financing activities ​ ​ ​ ​ ​ ​ Proceeds from follow-on public offering of ordinary shares, net of issuance costs ​ ​ 242,681 ​ ​ 80,511 Proceeds from issuance of ordinary shares related to employee stock options and purchase plans ​ ​ 6,985 ​ ​ 203 Net cash generated from financing activities ​ ​ 249,666 ​ ​ 80,714 Currency effect on cash, cash equivalents and restricted cash ​ ​ ( 1,906 ) ​ ​ 5,052 Net increase in cash, cash equivalents and restricted cash ​ ​ 332,760 ​ ​ 94,943 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 ​ $ 414,561 ​ $ 255,272 Cash and cash equivalents ​ $ 413,027 ​ $ 253,778 Restricted cash related to leasehold and other deposits ​ ​ 1,534 ​ ​ 1,494 Total cash, cash equivalents and restricted cash ​ $ 414,561 ​ $ 255,272 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 11,494 ) ​ $ ( 9,652 ) ​ The accompanying notes are an integral part of these unaudited consolidated financial statements . ​ ​ 6 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 25, 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 parentheses, 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 and six months ended June 30, 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”). ​ 7 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; the disclosure of contingent liabilities at the date of the financial statements; and the 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 six months ended June 30, 2026. ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the six months ended June 30, 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 June 30, 2026 and December 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, 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) ​ $ 397,308 ​ $ 30 ​ $ — ​ $ 397,338 Total ​ $ 397,308 ​ $ 30 ​ $ — ​ $ 397,338 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 June 30, 2026 and December 31, 2025, no expected credit loss was identified with respect to the investment securities. ​ 8 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. ​ 9 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 June 30, 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 June 30, 2026 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 413,027 ​ $ — ​ $ — ​ $ 413,027 ​ Cash and cash equivalents Restricted cash ​ ​ 1,534 ​ ​ — ​ ​ — ​ ​ 1,534 ​ Other non-current assets Total assets ​ $ 414,561 ​ $ — ​ $ — ​ $ 414,561 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Liability related to pre-funded warrants ​ ​ — ​ ​ 24,242 ​ ​ — ​ ​ 24,242 ​ Liability related to pre-funded warrants Contingent consideration ​ ​ — ​ ​ — ​ ​ 18,113 ​ ​ 18,113 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 617 ​ ​ 617 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ 24,242 ​ $ 18,730 ​ $ 42,972 ​ ​ ​ a) Contingent consideration ​ The Company is required to pay up to EUR 143.1 million (or $ 163.0 million based on the foreign exchange rate on June 30, 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 June 30, 2026 was EUR 15.9 million ($ 18.1 million) (December 31, 2025: EUR 15.9 million ($ 18.7 million)) using discount rates of approximately 10.1 % to 11.8 % (December 31, 2025: 11.8 %). ​ If, as of June 30, 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 51.3 million ($ 58.4 million). If, as of June 30, 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. ​ 10 Table of Contents The following table presents the changes in fair value of the contingent consideration (presented within non-current liabilities) between December 31, 2025 and June 30, 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) ​ ​ ( 82 ) Currency translation effects ​ ​ ( 541 ) Balance at June 30, 2026 ​ $ 18,113 ​ The Company classified the total contingent consideration liability as non-current as of June 30, 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 increase in fair value (presented within Other non-operating (losses), net) ​ ​ 12,201 Currency translation effects ​ ​ ( 554 ) Balance at June 30, 2026 ​ $ 24,242 ​ ​ ​ 5 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Accruals for goods received from and services provided by vendors, not yet billed ​ $ 24,684 ​ $ 20,490 Personnel-related accruals and liabilities (As of June 30, 2026, $ 7.2 million (December 31, 2025: $ 0.0 million) related to cash proceeds from employees' stock option exercises) ​ ​ 16,654 ​ ​ 9,941 Liability owed to the Purchaser pursuant to the Royalty Financing Agreement (refer to Note 7, " Royalty Financing Agreement ") ​ ​ 5,778 ​ ​ 5,523 Current portion of firm purchase commitment liability (including Genezen CSA termination payment) ​ ​ 3,808 ​ ​ 5,102 Other current liabilities ​ ​ 209 ​ ​ 236 Total ​ $ 51,133 ​ $ 41,292 ​ ​ 11 Table of Contents In April 2026, the Company entered into an agreement to terminate the commercial supply agreement (the “Genezen CSA”) with Genezen MA, Inc. (together with Genezen Holdings Inc., “Genezen”). Pursuant to the termination agreement, our obligation to supply HEMGENIX ® and any minimum purchase commitments under the Genezen CSA terminate once contractually specified batches have been supplied. In connection with the termination, the Company wrote down the remaining carrying value of the intangible asset for the favorable supply terms under the Genezen CSA. The net effect of these items was recorded in Other expense, and did not have a material impact on the Company’s results of operations for the three and six months ended June 30, 2026. ​ ​ ​ ​ 6 Long-term debt ​ The total principal outstanding as of June 30, 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 $ 50.5 million as of June 30, 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 and six months ended June 30, 2026 was $ 0.5 million and $ 1.6 million, respectively, compared to a foreign currency gain of $ 4.3 million and $ 6.4 million, respectively, during the same periods in 2025. Interest expense during the three and six months ended June 30, 2026 was $ 1.4 million and $ 2.8 million, respectively, compared to $ 1.8 million and $ 3.6 million, respectively, during the same periods in 2025. During the six months ended June 30, 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 June 30, 2026, the Company was in compliance with all applicable covenants under the facility. In July 2026, subsequent to the balance sheet date, the Company entered into an amendment to its loan facility with Hercules Capital, Inc. (as amended, the “2026 Amended Facility”). The amendment extended the period during which the Company may draw the $ 100.0 million term loan tranche from June 15, 2027 to September 30, 2027. Except as provided for in the amendment, the terms of borrowing under the 2026 Amended Facility remained unchanged. ​ 7 Royalty Financing Agreement ​ During the six months ended June 30, 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 the Royalty Financing Agreement for the period from December 31, 2025 to June 30, 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 ​ ​ ( 9,195 ) Interest expense for the period ​ ​ 25,584 Balance as of June 30, 2026 (includes $ 5.8 million presented as "Accrued expenses and other current liabilities") ​ $ 495,111 ​ ​ The Company records the debt at amortized cost using the effective interest method based on projected cash flows. As of June 30, 2026, the effective interest rate is expected to be within a range of 10.0 % to 11.5 % per annum (June 30, 2025: 12.0 % to 13.5 %). Interest expense recorded in connection with the Royalty Financing Agreement was $ 13.0 million and $ 13.8 million for the three months ended June 30, 2026 and 2025, respectively, and $ 25.6 million and $ 27.1 million for the six months ended June 30, 2026 and 2025, respectively. ​ ​ 12 Table of Contents 8 Shareholders’ equity ​ In June 2026, the Company received net proceeds of $ 242.7 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company, through a follow-on public offering of 5.7 million ordinary shares, at a public offering price of $ 45.50 per ordinary share. ​ In June 2026, the Company's shareholders approved an amendment to the Articles of Association increasing the Company's authorized share capital from 80.0 million ordinary shares to 100.0 million ordinary shares with a nominal value of € 0.05 per share. ​ ​ 9 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 2026, the Company’s shareholders authorized an additional 350,000 ordinary shares for issuance under the 2014 Plan. As of June 30, 2026, a total of 2,815,628 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 June 30, ​ Six months ended June 30, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) ​ (in thousands) Research and development expenses ​ ​ 1,888 ​ ​ 2,758 ​ ​ 3,865 ​ ​ 5,221 Selling, general and administrative expenses ​ ​ 3,128 ​ ​ 2,326 ​ ​ 6,241 ​ ​ 4,273 Total ​ $ 5,016 ​ $ 5,084 ​ $ 10,106 ​ $ 9,494 ​ Share-based compensation expense recognized by award type for the 2014 Plans as well as the ESPP was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended June 30, ​ Six months ended June 30, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 1,861 ​ $ 1,662 ​ $ 3,668 ​ $ 3,299 Restricted share units ​ ​ 3,255 ​ ​ 2,547 ​ ​ 6,461 ​ ​ 4,760 Performance share units ​ ​ ( 108 ) ​ ​ 875 ​ ​ ( 46 ) ​ ​ 1,435 ESPP ​ ​ 8 ​ ​ — ​ ​ 23 ​ ​ — Total ​ $ 5,016 ​ $ 5,084 ​ $ 10,106 ​ $ 9,494 ​ 13 Table of Contents As of June 30, 2026, the unrecognized share-based compensation expense related to unvested awards under the 2014 Plans was: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized ​ Weighted average ​ ​ ​ ​ share-based ​ ​ ​ remaining ​ ​ compensation ​ period for ​ ​ expense ​ recognition ​ ​ (in thousands) ​ (in years) Award type ​ ​ ​ ​ ​ Share options ​ $ 14,464 ​ 2.57 Restricted share units ​ ​ 25,886 ​ 2.17 Performance share units ​ ​ 427 ​ 0.87 Total ​ $ 40,776 ​ 2.30 ​ 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 six months ended June 30, 2026: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ ​ ​ Number of ordinary shares ​ ​ ​ ​ Weighted average exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2025 ​ 4,531,991 ​ ​ 17.04 Granted ​ 869,760 ​ $ 11.48 Forfeited ​ ( 12,451 ) ​ $ 9.58 Expired ​ ( 16,186 ) ​ $ 37.84 Exercised ​ ( 410,849 ) ​ $ 16.60 Outstanding at June 30, 2026 ​ 4,962,265 ​ $ 16.05 Thereof, fully vested, and exercisable on June 30, 2026 ​ 2,769,675 ​ $ 19.77 Thereof, outstanding and expected to vest after June 30, 2026 ​ 2,192,590 ​ $ 11.35 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) ​ ​ ​ ​ ​ ​ ​ $ 6.4 ​ 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 June 30, ​ ​ ​ Six months ended June 30, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ ​ 2026 ​ ​ ​ 2025 Assumptions ​ ​ ​ ​ ​ ​ ​ ​ Expected volatility ​ 95 % ​ 80 % ​ 95 % ​ 70 % - 80 % Expected terms ​ 10 years ​ 10 years ​ 10 years ​ 10 years Risk-free interest rate ​ 4.68 % ​ 4.64 % ​ 4.21 % - 4.68 % ​ 4.36 % - 4.64 % Expected dividend yield ​ 0.0 % ​ 0.0 % ​ 0.0 % ​ 0.0 % ​ 14 Table of Contents RSUs ​ The following table summarizes the RSU activity for the six months ended June 30, 2026: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSUs ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2025 ​ 2,395,420 ​ $ 12.15 Granted ​ 1,112,250 ​ $ 12.36 Vested ​ ( 886,521 ) ​ $ 12.29 Forfeited ​ ( 113,350 ) ​ $ 16.22 Non-vested at June 30, 2026 ​ 2,507,799 ​ $ 12.01 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 13.8 ​ 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, would have been earned upon the Board of Directors’ assessment of the level of achievement of an agreed upon performance target, and, with respect to the 2026 PSUs, will be earned upon Company 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 June 30, 2026, certain 2026 PSUs were assessed as probable of achieving the requisite performance condition. ​ As of June 30, 2026, the Company determined that the performance target for the outstanding 2024 PSUs were not met within the contractually defined performance period and were consequently forfeited. ​ The following table summarizes the PSU activity for the six months ended June 30, 2026: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2025 ​ 22,500 ​ $ 15.40 Granted ​ 28,750 ​ $ 22.40 Vested ​ — ​ $ — Forfeited ​ ( 22,500 ) ​ $ 15.40 Non-vested at June 30, 2026 ​ 28,750 ​ $ 22.40 ​ ESPP ​ During the six months ended June 30, 2026, 13,939 ordinary shares were issued under the ESPP compared to nil ordinary shares issued during the same period in 2025. As of June 30, 2026, 72,773 ordinary shares remain available for issuance under the ESPP compared to a total of 86,712 ordinary shares as of June 30, 2025. ​ ​ 15 Table of Contents 10 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 June 30, ​ Six months ended June 30, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) ​ (in thousands) Revenue ​ $ 5,841 ​ $ 5,262 ​ $ 9,403 ​ $ 6,829 Less: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Employee related expenses ​ ( 16,960 ) ​ ( 14,525 ) ​ ( 33,746 ) ​ ( 28,741 ) Laboratory and development expenses ​ ​ ( 17,387 ) ​ ​ ( 15,593 ) ​ ​ ( 32,148 ) ​ ​ ( 31,560 ) Professional fees ​ ​ ( 1,756 ) ​ ​ ( 3,124 ) ​ ​ ( 6,263 ) ​ ​ ( 5,181 ) Information technology system costs (2) ​ ​ ( 1,427 ) ​ ​ ( 838 ) ​ ​ ( 3,086 ) ​ ​ ( 1,839 ) Facility expenses ​ ​ ( 1,437 ) ​ ​ ( 1,704 ) ​ ​ ( 2,984 ) ​ ​ ( 3,371 ) Other segment items (1) (2) ​ ​ ( 2,511 ) ​ ​ ( 1,804 ) ​ ​ ( 6,024 ) ​ ​ ( 2,773 ) Segment operating loss ​ ​ ( 35,637 ) ​ ​ ( 32,326 ) ​ ​ ( 74,848 ) ​ ​ ( 66,636 ) Reconciliation ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation and amortization expense ​ ​ ( 4,907 ) ​ ​ ( 3,630 ) ​ ​ ( 7,863 ) ​ ​ ( 8,157 ) Share-based compensation expense ​ ​ ( 5,016 ) ​ ​ ( 5,084 ) ​ ​ ( 10,106 ) ​ ​ ( 9,494 ) Fair value (loss) / gain - contingent consideration ​ ​ ( 1,256 ) ​ ​ ( 2,254 ) ​ ​ 82 ​ ​ ( 3,470 ) Fair value loss - Liability related to pre-funded warrants ​ ​ ( 15,970 ) ​ ​ — ​ ​ ( 12,201 ) ​ ​ — Foreign currency (losses) / gains, net ​ ​ ( 1,730 ) ​ ​ 18,638 ​ ​ ( 4,024 ) ​ ​ 25,810 Interest income ​ ​ 5,051 ​ ​ 3,524 ​ ​ 10,280 ​ ​ 7,651 Interest expense - Royalty Financing Agreement ​ ​ ( 12,963 ) ​ ( 13,770 ) ​ ​ ( 25,584 ) ​ ( 27,079 ) Interest expense - Hercules loan facility ​ ​ ( 1,403 ) ​ ​ ( 1,821 ) ​ ​ ( 2,813 ) ​ ​ ( 3,621 ) Other reconciling items ​ ​ ( 5,387 ) ​ ​ ( 571 ) ​ ​ ( 5,188 ) ​ ​ 4,561 Consolidated loss before income tax expense ​ $ ( 79,218 ) ​ $ ( 37,294 ) ​ $ ( 132,265 ) ​ $ ( 80,435 ) ​ (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 . (2) The comparative amounts for the three and six months ended June 30, 2025 have been adjusted to reflect the level of detail at which the CODM reviews segment operating expenses in 2026, with information technology system costs presented as a separate line item and consumables included within other segment items for all periods presented. ​ ​ 16 Table of Contents 11 Other investments and concentration of credit risk ​ The following table summarizes the Company’s other investments as of June 30, 2026 and December 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ ​ ​ ​ 2026 ​ ​ ​ 2025 ​ ​ (in thousands) Carrying amount of equity investments ​ $ 15,143 ​ $ 15,615 Convertible note receivable ​ ​ 15,124 ​ ​ 14,622 Total ​ $ 30,267 ​ $ 30,237 ​ 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 June 30, 2026 and December 31, 2025 was $ 15.1 million and $ 15.6 million, respectively, and are presented within Other Investments in the Company’s Consolidated Balance Sheets. The Company did not recognize any upward adjustments, downward adjustments, or impairments relating to investments carried under the measurement alternative during the three and six months ended June 30, 2026, and 2025. Genezen In 2024, as part of the Company’s divestment of its commercial manufacturing operations to Genezen, the Company entered into various service agreements including the Genezen CSA. In April 2026, the Company entered into an agreement to terminate the Genezen CSA. Pursuant to the termination agreement, the Company’s obligation to supply HEMGENIX ® and any minimum purchase commitments under the Genezen CSA terminate once contractually specified batches have been supplied. ​ The Company’s prepayments for services to be received amounted to $ 5.7 million as of June 30, 2026, compared to $ 13.9 million as of December 31, 2025. In addition, as of June 30, 2026, the Company holds a convertible note receivable of $ 15.1 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 and six months ended June 30, 2026 or 2025. ​ CSL Behring ​ As of June 30, 2026 and December 31, 2025, accounts receivable from CSL Behring LLC (“CSL Behring”) totaled $ 5.8 million and $ 5.9 million, respectively, in each case related to royalty revenue which is included in License Revenue in the accompanying statements of operations and comprehensive loss. ​ ​ ​ 12 Income taxes ​ The Company recorded a deferred tax expense of $ 1.8 million and $ 2.3 million related to its U.S. operations during the three and six months ended June 30, 2026 ($ 0.4 million and $ 0.9 million for the three and six months ended June 30, 2025). ​ The effective income tax rate of 2.3 % and 1.8 % during the three and six months ended June 30, 2026 (three and six months ended June 30, 2025: 1.1 % and 1.1 %, respectively) 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, among various other items which impacted the effective rate. ​ ​ 17 Table of Contents 13 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 and six months ended June 30, 2026, 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 and six months ended June 30, 2026. 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 June 30, 2026 and June 30, 2025, respectively. ​ The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended June 30, ​ Six months ended June 30, ​ 2026 ​ ​ ​ 2025 ​ ​ ​ 2026 ​ ​ ​ 2025 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans $ 4,962,265 ​ $ 5,321,862 ​ $ 4,962,265 ​ $ 5,321,862 Non-vested RSUs and PSUs ​ 2,536,549 ​ ​ 2,442,969 ​ ​ 2,536,549 ​ ​ 2,442,969 Pre-Funded Warrants ​ 526,316 ​ ​ — ​ ​ 526,316 ​ ​ — ESPP ​ 13,939 ​ ​ — ​ ​ 13,939 ​ ​ — Total anti-dilutive ordinary share equivalents ​ 8,039,069 ​ ​ 7,764,831 ​ ​ 8,039,069 ​ ​ 7,764,831 ​ ​ 14 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 are not fixed or determinable. 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 (collectively, “Defendants”) in the United States District Court for the Southern District of New York. The complaint purported to assert claims pursuant to Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), 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 (the “putative Class Period”). The plaintiff sought 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 Biologics License Application filing for AMT-130. On April 13, 2026, the court appointed the Oklahoma Firefighters Pension and Retirement System as lead plaintiff (the “Lead Plaintiff”). On July 15, 2026, the Lead Plaintiff filed an amended complaint. Like the earlier-filed complaint, the amended complaint purports to assert claims pursuant to Sections 10(b) and 20(a) of the Exchange Act and Rule 10b-5, on behalf of a putative class of investors who purchased or otherwise acquired the Company’s ordinary shares during the putative Class Period. Lead Plaintiff seeks unspecified damages allegedly caused by purported false and misleading statements and omissions with respect to the import and viability of data from the Company’s Phase I/II study of AMT-130 and available pathways to regulatory approval. Defendants’ motion to dismiss the amended complaint is currently due September 14, 2026. Management 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. The Company has not recorded any liability for any portion of this matter because the Company believes that liability is not probable and reasonably estimable at this time. 18 Table of Contents 15 Subsequent events ​ In July 2026, subsequent to the balance sheet date, the Company entered into an amendment to its loan facility with Hercules Capital, Inc. (as amended, the “2026 Amended Facility”). The amendment extended the period during which the Company may draw the $ 100.0 million term loan tranche from June 15, 2027 to September 30, 2027. Except as provided for in the amendment, the terms of borrowing under the 2026 Amended Facility remained unchanged. ​ ​ 19 Table of Contents