Indicate by check mark whether the registrant has filed a report on and attestation to its management’s assessment of the effectiveness of its internalcontrol over financial reporting under Section404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm that prepared or issued its audit report.☐ If securities are registered pursuant to Section12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in thefiling reflect the correction of an error to previously issued financial statements.☐ Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensationreceived by any of the registrant’s executive officers during the relevant recovery period pursuant to §240.10D-1(b).☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act).Yes☐No☒ The aggregate market value of the Registrant’s common equity held by non-affiliates, based upon the closing price of the Registrant’s securities on theNasdaq Capital Market of $12.63 on December31, 2024 was approximately $152,964,292 There were26,250,469shares of the Registrant’s common stock, $0.0001 par value per share, outstanding on September17, 2025. EXPLANATORY NOTE Benitec Biopharma Inc. is filing this Amendment No.1 (this “Form 10-K/A”) to its Annual Report on Form 10-K for the fiscal year ended June30, 2025(the “Original 10-K”), as originally filed with the Securities and Exchange Commission (the “Commission”) on September22, 2025, for the purpose ofincluding the conformed signature of Baker Tilly US, LLP on the Report of Independent Registered Public Accounting Firm (the “Report”) within Item8 of the Original 10-K. The conformed signature was inadvertently omitted from the version of the Report that was filed with the Original 10-K. ThisForm 10-K/A includes the Report with the conformed signature. The exhibit list appearing in Item 15 of the Form 10-K has been updated to indicate thatExhibits 21.1 and 97 were previously filed. This Form 10-K/A includes new certifications, as required by Rule 12b-15 under the Securities Exchange Except for the correction described above, this Form 10-K/A does not purport to update any disclosures contained in the annual report. For disclosuressubsequent to September22, 2025, please see the Company’s reports filed with the Commission after that date. Report of Independent Registered Public Accounting FirmBaker Tilly(PCAOB Firm ID No.23)Consolidated Balance Sheets Table of Contents REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM To the Stockholders and the Board of Directors of Benitec Biopharma Inc. Opinion on the Financial Statements We have audited the accompanying consolidated balance sheets of Benitec Biopharma Inc. (the “Company”) as of June30, 2025 and 2024, the relatedconsolidated statements of operations and comprehensive loss, stockholders’ equity and cash flows, for each of the two years in the period endedJune30, 2025, and the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial Basis for Opinion These consolidated financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on theCompany’s consolidated financial statements based on our audits. We are a public accounting firm registered with the Public Company AccountingOversight Board (United States) (“PCAOB”) and are required to be independent with respect to the Company in accordance with the U.S. federal We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtainreasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud. The Companyis not required to have, nor were we engaged to perform, an audit of its internal control over financial reporting. As part of our audits we are required to Our audits included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error orfraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts anddisclosures in the consolidated financial statements. Our audits also included evaluating the accounting principles used and significant estimates made Critical Audit Matter Critical audit matters are matters arising from the current period audit of the financial statements that were communicated or required to becommunicated to the audit committee and that: (1)relate to accounts or disclosures that are material to the financial statements and (2)involved our /s/ Baker Tilly US, LLP San Diego, CaliforniaSeptember22, 2025 We have served as the Company’s auditor since 2020. Table