enGene Holdings Inc.

Evaluation of Disclosure Controls and Procedures

As of the end of the period covered by this Annual Report, management, under the supervision of and with the participation of our Chief Executive Officer (principal executive officer) and Chief Financial Officer (principal financial officer and principal accounting officer), carried out an evaluation of the effectiveness of the design and operation of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) to determine whether such disclosure controls and procedures provide reasonable assurance that information to be disclosed by us in the reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the rules and forms of the SEC and such information is accumulated and communicated to management, including our principal executive and principal financial officers or persons performing similar functions, as appropriate to allow timely decisions regarding disclosure. Based on our assessment, management concluded that, as of October 31, 2025, our disclosure controls and procedures were effective.

Management’s Report on Internal Control Over Financial Reporting

Management is responsible for establishing and maintaining adequate internal control over financial reporting, as defined in Rule 13a-15(f) under the Exchange Act. Our internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of the financial statements for external purposes in accordance with U.S. GAAP. Our management, under the supervision of and with the participation of our Chief Executive Officer and Chief Financial Officer, conducted an evaluation of our internal control over financial reporting based on the framework in Internal Control—Integrated Framework issued in 2013 by the Committee of Sponsoring Organizations of the Treadway Commission. Based on this assessment, management concluded that, as of October 31, 2025, our internal control over financial reporting was effective.

This annual report does not include an attestation report of the Company’s registered public accounting firm as the Company’s status as an “emerging growth company” and a “non-accelerated filer” exempts it from such requirement, pursuant to established rules of the SEC.

Remediation Efforts to Address the Material Weakness

As previously reported, in connection with our preparation and the audit of our consolidated financial statements as of and for the years ended October 31, 2024 and 2023, we identified material weaknesses, as defined under the Exchange Act, in our internal control over financial reporting. The material weaknesses related to a lack of formal policies, procedures, and controls over financial reporting, a lack of sufficient accounting and financial reporting personnel with requisite knowledge of GAAP, general information technology controls that were not designed appropriately, and a lack of appropriate segregation of duties. A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting such that there is a reasonable possibility that a material misstatement of our consolidated financial statements will not be prevented or detected on a timely basis.

Based on the remediation efforts described below, these material weaknesses have been tested and determined to be remediated as of October 31, 2025. Remediation efforts included the following:

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hiring finance and accounting personnel with adequate experience and U.S. GAAP knowledge, including a Chief Financial Officer;

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establishing adequate review and approval processes and procedures based on the roles and responsibilities of each accounting members;

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implementing a risk assessment over financial reporting controls;

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designing and implementing policies, procedures and controls around key business and financial reporting process and general information technology controls;

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enhancing software tools to ensure segregation of duties; and

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engaging a professional accounting services firm to assist with the documentation and assessment of our internal controls for compliance with the Sarbanes-Oxley Act.

Inherent Limitations on Effectiveness of Controls

Our management, including our principal executive officer and principal financial officer, concluded that, as of October 31, 2025, our disclosure controls and procedures and internal control over financial reporting were effective at a reasonable assurance level. However, our management does not expect that effective disclosure controls and procedures or our internal control over financial reporting will prevent all errors and all fraud. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the control system are met. Furthermore, the design of a control system must reflect the fact that there are resource constraints, and the benefits of controls must be considered relative to their costs. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, have been detected. These inherent limitations include the realities that judgments in decision making can be faulty, and that breakdowns can occur because of a simple error or mistake. Additionally, controls can be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the controls. The design of any system of controls is also based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions; over time, controls may become inadequate because of changes in conditions, or the degree of compliance with policies or procedures may deteriorate.

Changes in Internal Control Over Financial Reporting

Other than the items discussed above with respect to the remediation of previously identified material weaknesses, there were no other changes in our internal control over financial reporting during the fourth quarter ended October 31, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.