Notice to Convene the Annual General Meeting of Shareholders of uniQure N.V. To be held at and organized by uniQure N.V. (the Company ), having its address at Meibergdreef 61, 1105 BA Amsterdam, the Netherlands, at 2.00

Notice to Convene the Annual General Meeting of Shareholders

To be held at and organized by uniQure N.V. (the Company ), having its address at Meibergdreef 61, 1105 BA Amsterdam, the Netherlands, at 2.00 p.m. CET on 10 June 2015.

Shareholders are invited to attend the Annual General Meeting of Shareholders of the Company (the AGM ) to be held on 10 June 2015 at 2.00 p.m. CET at the Company s offices in Amsterdam, the Netherlands. The language of the meeting will be English.

The agenda for the AGM and the explanatory notes (including the particulars of Mr. Astley-Sparke), together with the 2014 Annual Report including the 2014 statutory annual accounts are available for inspection at the offices of the Company, and will be distributed free of charge on request. The information is also available on the Company s website: www.uniqure.com, and at http://www.edocumentview.com/QURE.

ATTENDANCE AT THE ANNUAL GENERAL MEETING

Only holders of shares in the share capital of the Company as of the close of business on 13 May 2015 (the Record Date ) are entitled to vote at the AGM. Only shareholders who have given notice in writing to the Company by 5 June 2015 of their intention to attend the AGM in person are entitled to attend the AGM in person. Each share outstanding on the Record Date is entitled to one vote on each voting item.

For shareholders whose ownership is directly recorded in the Company s shareholders register (such shareholders, the Registered Shareholders ) and for shareholders holding their shares in an account at a bank, a financial institution, an account holder or other financial intermediary (such shareholders, the Beneficial Owners ), the conditions for attendance at the AGM are as follows:

Registered Shareholders must notify the Company by submitting their name and number of registered shares through the Company s email address ir@uniqure.com no later than on 5 June 2015; and

Beneficial Owners must have their financial intermediary or their agent with whom the shares are on deposit issue a proxy to them which confirms they are authorized to take part in and vote at the AGM. These Beneficial Owners must (i) notify the Company of their intention to attend by submitting their name and number of shares beneficially owned through the Company s email address ir@uniqure.com no later than on 5 June 2015 and (ii) bring the proxy received from their financial intermediary to the AGM.

Persons entitled to take part in the meeting may be asked for identification prior to being admitted to the AGM and are therefore asked to carry a valid identity document (such as a passport or driver s license).

PARTICIPATION IN THE ANNUAL GENERAL MEETING BY PROXY

Registered Shareholders who are not in a position to attend the meeting in person, may, without prejudice to the above registration and attendance notification provisions, grant a written proxy to

the following independent third party: Mr. H.B.H. Kraak of Holdinga Matthijssen Kraak, civil law notaries in Amsterdam, the Netherlands. The proxy can be granted with or without voting instructions. In case a proxy is granted to said independent party without voting instructions it shall be deemed to include a voting instruction in favour of all proposals made by the Management Board and/or the Supervisory Board of the Company, and against any other proposal. Proxy forms to be used to grant a written proxy are available free of charge at the offices of uniQure N.V. and at www.uniqure.com. To be counted, a duly completed and executed proxy must have been received by Mr. H.B.H. Kraak, at the offices of Holdinga Matthijssen Kraak or, if sent in pdf-form electronically at his email address: bk@hmknotarissen.nl with the original to follow by regular mail, in each case no later than on 5 June 2015, at 23:59 hrs CET. These shareholders or their representatives will receive a confirmation of registration from the Company.

Beneficial Owners who wish to exercise their voting rights by proxy should follow the instructions and use the voting instrument provided by the bank, financial institution, account holder or other financial intermediary that holds the shares on such Beneficial Owner s behalf.

For further information, please contact: uniQure N.V., Corporate Secretary, Meibergdreef 61, 1105 BA Amsterdam, the Netherlands, email: ir@uniqure.com.

Amsterdam, the Netherlands, 6 May 2015

The Management Board

Agenda for the Annual General Meeting on 10 June 2015 at 2.00 p.m. CET, at Meibergdreef 61, 1105 BA in Amsterdam, the Netherlands.

1. Opening and announcements

2. Report of the Management Board for the financial year 2014 (discussion item)

3. Explanation of the application of the remuneration policy (discussion item)

4. Adoption of the 2014 annual accounts (voting item)

5. Discharge of liability of the members of the Management Board for their management (voting item)

6. Discharge of liability of the members of the Supervisory Board for their supervision (voting item)

7. Reappointment of PricewaterhouseCoopers Accountants N.V. ( PwC ), an independent registered public accounting firm, as auditors of the Company for 2015 (voting item)

8. Appointment of Mr. Kapusta as member of the Management Board (voting item)

9. Appointment of Mr. Astley-Sparke as member of the Supervisory Board (voting item)

10. Remuneration of the Supervisory Board (voting item)

11. Designation of the Management Board as the competent body to issue ordinary shares and options and to limit or exclude pre-emptive rights (voting item)

12. Issuance of (rights to) ordinary shares to Bristol-Myers Squibb and exclusion of pre-emptive rights in connection therewith (voting item)

13. 2014 Share Incentive Plan

a. Amendment of the 2014 Share Incentive Plan (voting item)

b. Designation of the Supervisory Board as the competent body to issue ordinary shares and options and to exclude pre-emptive rights under the Amended Plan (voting item)

14. Authorization of the Management Board to repurchase ordinary shares (voting item)

15. Any other business

16. Closing of the meeting

Explanatory notes to the agenda for the Annual General Meeting of Shareholders ( AGM ) of uniQure N.V. ( uniQure or the Company ) to be held on 10 June 2015 at 2.00 p.m. CET, at Meibergdreef 61, 1105 BA Amsterdam, the Netherlands.

These explanatory notes and other information are available for inspection as of the date hereof. These items can be obtained free of charge at the Company s office address and are also available at the Company s website: www.uniqure.com.

Agenda item 2: Report of the Management Board for the 2014 financial year

Under this agenda item, the Management Board will discuss the report on the 2014 financial year (the 2014 Annual Report ). In accordance with the Dutch Corporate Governance Code, the contents of the corporate governance chapter in the 2014 Annual Report, including the Company s compliance with the Dutch Corporate Governance Code, are also tabled for discussion.

Agenda item 3: Explanation of the application of the remuneration policy

Under this agenda item, an explanation will be provided on how the remuneration policy for the Management Board has been applied in 2014. Relevant information on the remuneration of the members of the Management Board is included in the 2014 Annual Report beginning on page 38.

Agenda item 4: Adoption of the 2014 annual accounts

It is proposed to the General Meeting to adopt the annual accounts for the 2014 financial year. These accounts were prepared by the Management Board and audited and provided with an unqualified auditor s report by PricewaterhouseCoopers Accountants N.V., the Company s external auditor (page 119 of the 2014 Annual Report). The 2014 Annual Report, including the annual accounts, has been made available to the General Meeting at the time notice of this meeting was given.

Agenda items 5 and 6: Discharge of liability of the members of the Management Board and Supervisory Board

The discharge of the members of the Management Board and the discharge of the members of the Supervisory Board are two separate items on the agenda.

It is proposed to grant discharge to the members of the Management Board for the management and conducted policy during the 2014 financial year insofar as the exercise of such duties is reflected in the 2014 Annual Report or otherwise disclosed to the General Meeting. It is also proposed to grant discharge to the members of the Supervisory Board for their supervision of the policies of the Management Board and the general course of affairs of the Company and its affiliated business during the financial year 2014 insofar as the exercise of such duties is reflected in the 2014 Annual Report or otherwise disclosed to the General Meeting.

Agenda item 7: Reappointment of PwC as auditors of the Company for the 2015 financial year ending at the close of the AGM in 2016

It is proposed to reappoint PricewaterhouseCoopers Accountants N.V., an independent registered public accounting firm, as the external auditor charged with the auditing of the annual accounts for the 2015 financial year.

Agenda item 8: Appointment of Mr. Kapusta as member of the Management Board

The Supervisory Board has resolved, on the recommendation of the Nominating and Corporate Governance Committee, to nominate Mr. Kapusta for appointment in the position of member of the Management Board of the Company for a term ending at the end of the 2019 AGM. Mr. Kapusta has joined the Company s management team as Chief Financial Officer as of 1 January 2015.

Mr. Kapusta joined uniQure from Angiodynamics, where he was Senior Vice President responsible for corporate development, strategic planning and national accounts. Prior to this, he served as Vice President, Finance, for Smith & Nephew Orthopaedics. He previously held several positions in investment banking and equity, including his role as Managing Director, Healthcare Investment Banking at Collins Stewart, and leadership positions at Wells Fargo Securities and Robertson Stephens. Mr. Kapusta holds a Master in Business Administration from New York University and an undergraduate degree in business from University of Michigan.

Given his experience and expertise we believe Mr. Kapusta will be a valuable addition to our Management Board.

Below is an overview of the main elements of Mr. Kapusta s employment agreement, including the remuneration package of Mr. Kapusta. The remuneration package is in accordance with the Company s remuneration policy and with the Dutch Corporate Governance Code.

Agenda item 9: Appointment of Mr. Astley-Sparke as member of the Supervisory Board

The Supervisory Board has resolved, on the recommendation of the Nominating and Corporate Governance Committee, to nominate Mr. Astley-Sparke for appointment in the position of member of the Supervisory Board of the Company for a term ending at the end of the 2018 AGM.

Philip Astley-Sparke (1971) has served as the president of the Company s United States operations from January 2013 to the end of January 2015. Mr. Astley-Sparke has been a venture partner at Forbion Capital Partners, a venture capital fund, since May 2012. He served as vice president and general manager at Amgen, Inc., a biopharmaceutical company, until December 2011, following Amgen s acquisition of BioVex Group, Inc., a biotechnology company, in March 2011. Mr. Astley-Sparke had been president and chief executive officer of BioVex Group since 2007, which he joined in 2000, and previously served in roles of President, COO and CFO where he oversaw the company s relocation to the U.S. Prior to BioVex, Mr. Astley-Sparke was a

healthcare investment banker at Chase H+Q/Robert Fleming. He qualified as a chartered accountant with Arthur Andersen in London and holds a bachelor s degree in cellular pathology and molecular pathology from Bristol University in the United Kingdom. He also serves as chairman of the board of Oxyrane, a biotechnology company.

Mr. Astley-Sparke holds no ordinary shares in the Company and options to purchase 85,200 ordinary shares as of 4 May 2015.

Given his experience and expertise we believe Mr. Astley-Sparke will be a valuable addition to our Supervisory Board.

The Supervisory Board has the intention to elect Mr. Astley-Sparke as a member of the Nominating and Corporate Governance Committee.

In a press release dated 9 January 2015 it was announced that Dr. Hugo Katus had agreed to be nominated for appointment to the Supervisory Board. The Company and Dr. Katus have mutually agreed to not propose him for appointment as a member of the Supervisory Board. The Company is delighted, however, that Dr. Katus will continue to serve as Chairman of the Scientific Advisory Board for cardiovascular diseases.

Agenda item 10: Remuneration of the Supervisory Board

The remuneration of the Supervisory Board is reviewed on an annual basis by the Remuneration Committee. In order to align the remuneration of the Supervisory Board with market developments with respect to the remuneration of non-executive directors, it is proposed to the General Meeting to award an annual fixed component effective as per 1 January 2015 according to the fixed remuneration schedule below:

The above fixed remuneration will also apply to newly appointed members. Fees for attendance in person or by telephone at each Supervisory Board meeting will no longer be paid. The increase of the fixed remuneration component is based on an evaluation of the annual remuneration for non-executive directors of a comparator group, consisting of NASDAQ listed companies operating in the same field of operations as the Company and of comparable size.

It is further proposed that the General Meeting approves the resolution of the Supervisory Board dated 9 July 2014 to grant to each member of the Supervisory Board as of that date - subject to the approval by the General Meeting - an option to acquire up to 5,000 ordinary shares in the capital of the Company.

Agenda item 11: Designation of the Management Board as the competent body to issue ordinary shares and options and to limit or exclude pre-emptive rights

It is proposed that the Management Board is designated as the competent body to issue ordinary shares in the share capital of the Company having a nominal value of EUR 0.05 per share ( ordinary shares ) and to grant rights to subscribe for ordinary shares for a term of 18 months with effect from 10 June 2015, and to limit or exclude pre-emptive rights in connection therewith, all subject to the approval of the Supervisory Board. The number of ordinary shares to be issued

shall be limited to a maximum of 19.9% of the Company s aggregate issued capital at the time of issuance (less any shares previously issued pursuant to such authority).

This designation will allow the Management Board to be flexible and react quickly in respect of the financing of the Company, if and when deemed appropriate, without additional approval from the shareholders. The designation can be used for any and all purposes, subject to statutory limitations and with the exception of awards under the 2014 Plan (as defined under item 13 of this agenda), for which the Supervisory Board has been authorized by the General Meeting of Shareholders of 20 January 2014 for the duration of the 2014 Plan. Reference is made to item 13(a) of this agenda for a proposed amendment of this authorization.

The Management Board and the Supervisory Board unanimously recommend that the shareholders vote in favor of agenda item 11.

Agenda item 12: Issuance of (rights to) ordinary shares in connection with the BMS Transaction and exclusion of pre-emptive rights in connection therewith

Bristol-Myers Squibb Collaboration

On 6 April 2015, uniQure entered into a series of agreements with Bristol-Myers Squibb ( BMS ), a publicly traded global biopharmaceutical company, regarding a collaboration that provides BMS with exclusive access to the Company s gene therapy technology platform for multiple targets in cardiovascular and potentially other diseases. As part of this collaboration, BMS also agreed to make an equity investment in the Company.

Collaboration and License Agreement

Under the Collaboration and License Agreement with BMS, uniQure will provide BMS with exclusive access to uniQure s proprietary gene therapy program for congestive heart failure. The collaboration includes uniQure s proprietary congestive heart failure gene therapy candidate, which has demonstrated in advanced preclinical models that it can restore the ability to synthesize S100A1, a calcium sensor and master regulator of heart function, and increase survival rates after myocardial infarction. In addition, uniQure will collaborate with BMS on up to nine additional gene therapy targets addressing a broad range of heart conditions and other target-specific disease areas. uniQure will be responsible for discovery, preclinical development, and CMC, and will provide BMS its vector technologies and access to its industrial, proprietary insect-cell based manufacturing platform. uniQure will be responsible for CMC portions of regulatory filings and will co-operate with BMS in the preparation of all regulatory materials and interactions with regulatory authorities. BMS will be responsible for clinical development and all commercial activities across all programs.

The financial terms include guaranteed, near-term payments to uniQure of approximately USD 100 million, including an upfront payment of USD 50 million to be made at the closing of the transaction. The closing of the transaction is expected to occur in the second quarter of 2015 subject to Hart-Scott-Rodino clearance and customary closing conditions. An additional USD 15 million payment is to be received within three months of the closing for the selection of three additional collaboration targets, in addition to the S100A1 program.

uniQure will be eligible to receive research, development and regulatory milestone payments, including up to USD 254 million for the lead S100A1 therapeutic and up to USD 217 million for each other gene therapy product potentially developed under the collaboration, assuming designation of all targets by BMS and satisfaction of all milestones. uniQure is also eligible to receive target designation fees, net sales based milestone payments and tiered single- to double-digit royalties on product sales.

The parties have also agreed to enter into a supply contract, under which uniQure will undertake the manufacturing of all gene therapy products under the collaboration.

As part of the collaboration, pursuant to a Share Subscription Agreement, BMS will acquire at the initial closing (the Initial Closing ) a number of uniQure s ordinary shares equal to 4.9% of uniQure s outstanding ordinary shares immediately following such issuance, at an acquisition price of USD 33.84 per share. Furthermore, prior to 31 December 2015, BMS will acquire a number of additional ordinary shares that, together with the shares acquired at the Initial Closing, would equal 9.9% of the outstanding ordinary shares immediately following such acquisition (the Second Closing ), at an acquisition price equal to the volume-weighted average price for the 20 trading days ending on the date that is five trading days prior to such acquisition, plus a 10% premium.

The Company has also granted BMS two warrants ( Warrant 1 and Warrant 2 ). Pursuant to Warrant 1, BMS may acquire an additional number of shares that, together with the shares acquired at the Initial Closing and Second Closing, would equal 14.9% of the outstanding ordinary shares immediately after such issuance. Pursuant to Warrant 2, BMS may acquire an additional number of shares that, together with the shares acquired at the Initial Closing and Second Closing and upon exercise of Warrant 1, would equal 19.9% of the outstanding ordinary shares immediately after such issuance. The subscription price per ordinary share pursuant to each of Warrant 1 and Warrant 2 will equal the greater of (x) the volume-weighted average price for the 20 trading days ending on the date that is five trading days prior to each such exercise, plus a 10% premium, and (y) USD 33.84 multiplied by a compound annual growth rate of 10% from the Initial Closing. The exercise of each warrant is conditioned upon the designation of additional collaboration targets and payment of related fees by BMS under the Collaboration and License Agreement. The Share Subscription Agreement, Warrant 1, Warrant 2 and the Investor Agreement (as defined below) are herein referred to as the Equity Agreements .

uniQure also entered into an investor agreement (the Investor Agreement ) with BMS regarding the rights and restrictions relating to the ordinary shares to be acquired by BMS, including certain stand still restrictions that restrict BMS from acquiring ordinary shares in addition to the ordinary shares acquired under the Equity Agreements, subject to certain exceptions.

BMS is also subject to a lock-up pursuant to the Investor Agreement that restricts BMS, without uniQure s prior consent, from selling or disposing of the ordinary shares it acquired for a certain period. This lock-up will in any event terminate in the event the Collaboration and License Agreement is terminated.

The Investor Agreement also requires BMS to vote all of the ordinary shares it beneficially holds in favor of all items on the agenda for the relevant general meeting of shareholders of the Company as proposed on behalf of the Company, subject to certain exceptions including certain change of control transactions. This voting provision will terminate upon the earlier of the date on which BMS no longer beneficially owns at least 4.9% of the outstanding ordinary shares, a transaction that provides BMS exclusive and absolute discretion to vote the ordinary shares it beneficially holds, and the termination of the Collaboration and License Agreement for breach by uniQure.

For further information on the Equity Agreements, reference is made to uniQure s Annual Report 2014 on Form 20-F.

As part of the performance by the Company of its obligations under the Equity Agreements, it is proposed and unanimously recommended by the Management Board and the Supervisory Board that the General Meeting hereby resolves:

1. to issue such number of ordinary shares at the Initial Closing as is equal to 4.9% of aggregate number of issued ordinary shares immediately following such issuance, at a subscription price of USD 33.84 per ordinary share, and to exclude the pre-emptive rights in connection therewith;

2. to issue such number of ordinary shares at the Second Closing as would, together with the shares acquired at the Initial Closing, equal 9.9% of the outstanding ordinary shares immediately following such issuance, at a subscription price equal to the volume-weighted average price for the 20 trading days ending on the date that is five trading days prior to such issuance, plus a 10% premium, and to exclude the pre-emptive rights in connection therewith;

3. to grant Warrant 1 and to issue such number of ordinary shares upon the exercise of Warrant 1 as would, together with the shares acquired at the Initial Closing and Second Closing, equal 14.9% of the outstanding ordinary shares immediately after such issuance, at a subscription price equal to the greater of (x) the volume-weighted average price for the 20 trading days ending on the date that is five trading days prior to each such exercise, plus a 10% premium, and (y) USD 33.84 multiplied by a compound annual growth rate of 10% from the Initial Closing, and to exclude the pre-emptive rights in connection therewith; and

4. to grant Warrant 2 and to issue such number of ordinary shares upon the exercise of Warrant 2 as would, together with the shares acquired at the Initial Closing and Second Closing and upon exercise of Warrant 1, equal 19.9% of the outstanding ordinary shares immediately after such issuance, at a subscription price equal to the greater of (x) the volume-weighted average price for the 20 trading days ending on the date that is five trading days prior to each such exercise, plus a 10% premium, and (y) USD 33.84 multiplied by a compound annual growth rate of 10% from the Initial Closing, and to exclude the pre-emptive rights in connection therewith,

all at such dates and in accordance with the terms and subject to the conditions as the Management Board will determine in the relevant deeds effecting the respective issuances of ordinary shares, pursuant to the terms and conditions of the Equity Agreements.

Agenda item 13: 2014 Share Incentive Plan

13a: Amendment of the 2014 Share Incentive Plan

The uniQure 2014 Share Incentive Plan (the 2014 Plan ) was approved by the Company s general meeting of shareholders on 9 January 2014. The purpose of the 2014 Plan is to advance the interests of the Company s shareholders by enhancing the Company s ability to attract, retain and motivate persons who are expected to make important contributions to the group and by providing such persons with equity ownership opportunities and performance-based incentives that are intended to better align the interests of such persons with those of the Company s shareholders. Pursuant to the 2014 Plan, the Company may grant incentive share options, non-statutory share options, share appreciation rights, restricted share awards, restricted share units and other share-based awards. Under the 2014 Plan, the maximum number of

ordinary shares available is currently limited to 1,531,471. As of 4 May 2015, 185,221 ordinary shares remain available for grant under the 2014 Plan.

It is now proposed to increase the option pool under the 2014 Plan in order to provide adequate incentives for new and existing employees, directors, consultants and advisors in light of the significant growth of the group s operations and staff since the time of the Company s initial public offering, as well as anticipated continued growth to support the Company s development programs.

The amendment to the 2014 Plan (the Amended Plan ), if approved, will increase the authorized number of ordinary shares available under the Plan by 1,070,000. It is also proposed to make certain technical changes in the Amended Plan, as described below.

A copy of the Amended Plan is available on the Company s website: www.uniqure.com.