Financial Analysis

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 Companys ordinary shares between September 24, 2025 and October 31, 2025 (the putative Class Period …

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9 Share-based compensation The Companys 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 Companys 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 Companys 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 mo …

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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 Companys 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 instruments 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 …

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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. …

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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 Companys 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 …

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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 Companys unaudited consolidated financial statements. …

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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 segmen …

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2.4 Accounting policies The principal accounting policies applied in the preparation of these unaudited consolidated financial statements are described in the Companys 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 Companys significant accounting policies during the six months ended June 30, 2026. …

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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. …

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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. …

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