ACCURAY INC 10-K/A

Item 9A. CONTROLS AND PROCEDURES Evaluation of Disclosure Controls and Procedures At the time the Original Filing was filed on the Original Filing Date, our management, with the participation of our Chief Executive Officer and Chief Financial Officer, evaluated the effectiveness of the design and operation of our disclosure controls and procedures (as defined in Rule 13a15(e) of the Exchange Act) as of the end of the period covered by our Annual Report on Form 10-K for the fiscal year ended June 30, 2025 (the “Evaluation Date”). Based on this evaluation, as of the Original Filing Date, our Chief Executive Officer and Chief Financial Officer concluded that as of the Evaluation Date, our disclosure controls and procedures were effective to provide reasonable assurance that the information required to be disclosed by us in the reports we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in the SEC’s rules and forms, and that such information is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer, as appropriate to allow timely decisions regarding required disclosure. Subsequent to this evaluation, in connection with the errors described in the Explanatory Note to this Form 10-K/A, and described further below, our Chief Executive Officer and Chief Financial Officer re-evaluated the effectiveness of our disclosure controls and procedures as of the end of the period covered by this report. Based upon that evaluation, our Chief Executive Officer and Chief Financial Officer have concluded that our disclosure controls and procedures were not effective as of June 30, 2025 due to the material weaknesses in internal control over financial reporting described below. Management ’ s Report on Internal Control over Financial Reporting Management is responsible for establishing and maintaining adequate internal control over financial reporting, as such term is defined in Rule 13a15(f) of the Exchange Act. Under the supervision and with the participation of the Chief Executive Officer and Chief Financial Officer, management conducted an evaluation of the effectiveness of our internal control over financial reporting based upon the guidelines established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO”) 2013. Based on this evaluation, at the time of Original Filing on August 28, 2025, management concluded that as of June 30, 2025 our internal control over financial reporting was effective. Subsequent to filing the Original Filing, management discovered errors related to the disclosure of remaining performance obligations (“RPO”) included in Note 2, Revenue, within previously filed Form 10-K and Form 10-Q. The errors were primarily due to the methodology applied for determining whether executed open system orders, upgrade sales orders, and customer credits represent remaining performance obligations in accordance with ASC 606, Revenue from Contracts with Customers . Based on management’s reevaluation of its methodology, it was determined that the Company incorrectly included these balances within the RPO footnote as the level of nonrefundable customer deposits at order execution relative to the total order value does not represent substantive termination penalties and therefore should be excluded from the RPO balances included within the disclosure. The Company has identified material weaknesses related to 1) the review of the footnote schedules supporting financial statement disclosures and 2) inadequate controls to appropriately analyze all relevant information required for complete and accurate presentation and disclosure under GAAP principally resulting from incorrect assessment during the initial adoption of ASC 606. Based on these two material weaknesses, management re-evaluated the effectiveness of internal control over financial reporting and concluded that as of June 30, 2025 the Company had not maintained effective internal control over financial reporting due to these two material weaknesses. 91 Table of Contents The effectiveness of our internal control over financial reporting as of June 30, 2025 has been audited by Grant Thornton LLP, as stated in their report included herein. Remediation Measures To remediate the material weakness resulting from the deficiency in the footnote disclosure review process described above, management has designed and is in the process of implementing enhanced review controls specific to financial statement footnote disclosures. These enhancements are intended to ensure greater precision in preparing and reviewing financial statement footnote disclosures, including additional reviewer involvement and targeted training for personnel responsible for review of the footnote schedules supporting the financial statement disclosures. Management has begun implementing these remediation efforts and will continue to evaluate and modify the remediation plan as appropriate. To remediate the material weakness resulting from the deficiency in management’s analysis of information for complete and accurate presentation and disclosure described above, management has designed and is in the process of implementing enhanced controls to ensure all relevant information required for complete and accurate presentation and disclosure, including the initial assessment of the impact of adopting new accounting pronouncements, is appropriately analyzed. Management has begun implementing these remediation efforts and will continue to evaluate and modify the remediation plan as appropriate. The Company will consider the above material weaknesses remediated when the enhanced controls have operated for a sufficient period of time and management has concluded that these controls are operating effectively. Remediation of Previously Disclosed Material Weaknesses As noted in our 2024 Annual Report on Form 10-K (the “2024 Annual Report”), management identified a material weakness within our system of internal control over financial reporting due to our SAP S/4HANA ERP system not being designed for and not maintaining effective controls to ensure that all manual journal entries consistently enforced segregation of duties in the approval process prior to being posted to the general ledger system. Remediation of this material weakness was completed during the three months ended December 31, 2024, and included establishing new controls and procedures to ensure segregation of duties is maintained between the creation, posting and approval of manual journal entries. As of December 31, 2024, these control activities have been appropriately designed and implemented, and have operated effectively for a sufficient period of time to conclude that the previously identified material weakness has been remediated. Also as noted in our 2024 Annual Report, management identified a second material weakness within our system of internal control over financial reporting due to our SAP S/4HANA ERP system not being designed for and not maintaining effective controls to ensure the existence of inventory at the Madison manufacturing warehouse locations because its controls relied on a cycle count program that, due to initial limitations associated with certain ERP system reports, was not sufficiently precise. This material weakness was remediated as of March 31, 2025, which included establishing new controls to allow for full capture of inventory with proper count timing required for an effective cycle count program, inclusive of reinforcement for proper cycle count process through policy statements, regular communications and periodic reviews and meetings with managers and staff. As of March 31, 2025, these control activities have been appropriately designed and implemented, and have operated effectively for a sufficient period of time to conclude that the previously identified material weakness has been remediated. Furthermore, the remediation of the two material weaknesses associated with the aforementioned control activities resulted from the remediation of the deficiency in the risk assessment component of the COSO framework disclosed in our 2024 Annual Report, which we remediated by performing a comprehensive risk analysis of the affected areas and implemented control activities that effectively managed the risks. Management has concluded that the Company’s consolidated financial statements included in this Annual Report on Form 10-K/A fairly present, in all material respects, our financial position, results of operations and cash flows for the periods presented with accounting principles generally accepted in the United States of America. Changes in Internal Control over Financial Reporting Our management, with the participation of our Chief Executive Officer and Chief Financial Officer, has evaluated any changes in our internal control over financial reporting that occurred during the year ended June 30, 2025, and has concluded that other than the changes described above under "Remediation of Previously Disclosed Material Weaknesses" and the new material weaknesses identified and described above there were no other changes in our internal control over financial reporting that occurred that have materially affected, or is reasonably likely to materially affect, our internal control over financial reporting. Inherent Limitations of Internal Controls Internal control over financial reporting cannot provide absolute assurance of achieving financial reporting objectives because of its inherent limitations. Internal control over financial reporting is a process that involves human diligence and compliance and is subject to lapses in judgment and breakdowns resulting from human failures. Internal control over financial reporting also can be circumvented by collusion or improper management override. Because of such limitations, there is a risk that material misstatements may not be prevented or detected on a timely basis by internal control over financial reporting. However, these inherent limitations are known features of the financial reporting process. Therefore, it is possible to design into the process safeguards to reduce, though not eliminate, this risk. 92 Table of Contents REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM Board of Directors and Stockholders Accuray Incorporated Opinion on internal control over financial reporting We have audited the internal control over financial reporting of Accuray Incorporated (a Delaware corporation) and subsidiaries (the “Company”) as of June 30, 2025, based on criteria established in the 2013 Internal Control — Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO”). In our opinion, because of the effect of the material weaknesses described in the following paragraphs on the achievement of the objectives of the control criteria, the Company has not maintained effective internal control over financial reporting as of June 30, 2025, based on criteria established in the 2013 Internal Control— Integrated Framework issued by COSO. A material weakness is a deficiency, or combination of control deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of the company’s annual or interim financial statements will not be prevented or detected on a timely basis. The following material weaknesses have been identified and included in management’s assessment. The Company did not operate effective controls over the review of financial statement disclosures. Specifically, the Company has identified material weaknesses related to 1) the review of the footnote schedules supporting financial statement disclosures and 2) inadequate controls to appropriately analyze all relevant information required for complete and accurate presentation and disclosure under GAAP principally resulting from incorrect assessment during the initial adoption of ASC 606. In our report dated August 28, 2025, we expressed an unqualified opinion that the Company maintained, in all material respects, effective internal control over financial reporting as of June 30, 2025, based on criteria established in the 2013 Internal Control—Integrated Framework issued by COSO. Management has subsequently identified a control deficiency involving the review of footnote disclosures. As a result, management has revised its assessment, as presented in the accompanying Management's Report on Internal Control over Financial Reporting, to conclude that the Company’s internal control over financial reporting was not effective as of June 30, 2025. Accordingly, our present opinion on the effectiveness of internal control over financial reporting as of June 30, 2025, as expressed herein, is different from that expressed in our previous report. We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (“PCAOB”), the consolidated financial statements of the Company as of and for the year ended June 30, 2025. The material weaknesses identified above was considered in determining the nature, timing, and extent of audit tests applied in our audit of the 2025 consolidated financial statements, and this report does not affect our report dated August 28, 2025, except for the “Remaining Performance Obligations” included in Note 2, as to which the date is February 17, 2026 which expressed an unqualified opinion on those financial statements. Basis for opinion The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Management’s Report on Internal Control over Financial Reporting. Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion. Definition and limitations of internal control over financial reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. /s/ GRANT THORNTON LLP San Jose, California August 28, 2025, except for the material weaknesses described in the third paragraph above, as to which the date is February 17, 2026 93 Table of Contents PART IV Item 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES (a) We have filed the following documents as part of this report: 1. Consolidated Financial Statements (as set forth in Item 8) Page No. Report of Independent Registered Public Accounting Firm (PCAOB ID 248) 46 Consolidated Balance Sheets 48 Consolidated Statements of Operations and Comprehensive Income (Loss) 49 Consolidated Statements of Stockholders’ Equity 50 Consolidated Statements of Cash Flows 51 Notes to Consolidated Financial Statements 53 2. Consolidated Financial Statement Schedules All financial statement schedules have been omitted, since the required information is not applicable or is not present in amounts sufficient to require submission of the schedule, or because the information required is included in the consolidated financial statements and notes thereto included in this Annual Report on Form 10-K. 3. Exhibits The following exhibits are incorporated by reference or filed herewith. Incorporated by Reference Exhibit No. Exhibit Description Form File No. Exhibit Filing Date Furnished or Filed Herewith 3.1 Amended and Restated Certificate of Incorporation of Registrant. 8-K 001-33301 3.1 02/06/2013 3.2 Amended and Restated Bylaws of Registrant. 8-K 001-33301 3.1 09/20/2023 4.1 Form of Common Stock Certificate. S-1/A 333-138622 4.3 02/05/2007 4.2 Indenture, dated as of May 13, 2021, between the Registrant and The Bank of New York Mellon Trust Company, N.A., as trustee . 8-K 001-33301 4.1 05/18/2021 4.3 Form of 3.75% Convertible Senior Note due 2026 (included in Exhibit 4.2) 8-K 001-33301 4.2 05/18/2021 4.4 Description of the Registrant’ s Securities 10-K 001-33301 4.7 09/07/2023 4.5 Form of Premium Warrant 8-K 001-33301 4.1 06/06/2025 4.6 Form of Penny Warrant 8-K 001-33301 4.2 06/06/2025 4.7 Form of DDTL Premium Warrant 8-K 001-33301 4.3 06/06/2025 4.8 Form of DDTL Penny Warrant 8-K 001-33301 4.4 06/06/2025 10.1 Office Lease between Old Sauk Trails Park Limited Partnership and TomoTherapy Incorporated, dated October 22, 2001. 10-K 001-33301 10.1 09/07/2023 10.2 First Amendment to Lease between Old Sauk Trails Park Limited Partnership and TomoTherapy Incorporated, dated May 1, 2004. 10-K 001-33301 10.2 09/07/2023 94 Table of Contents Incorporated by Reference Exhibit No. Exhibit Description Form File No. Exhibit Filing Date Furnished or Filed Herewith 10.3 Second Amendment to Lease between Old Sauk Trails Park Limited Partnership and Accuray, Inc FKA TomoTherapy, Inc., dated October 19, 2016. 10-K 001-33301 10.3 09/07/2023 10.4 Third Amendment to Lease between Old Sauk Trails Park Limited Partnership and Accuray Incorporated, dated March 27, 2020. 10-K 001-33301 10.4 09/07/2023 10.5 Fourth Amendment to Lease Deming Way Property Group LLC and Accuray Incorporated, dated August 19, 2022. 10-K 001-33301 10.5 09/07/2023 10.6 Accuray Incorporated 1998 Equity Incentive Plan and forms of agreements relating thereto. S-1 333-138622 10.4 11/13/2006 10.7* Accuray Incorporated 2007 Incentive Award Plan. 10-K 001-33301 10.8 09/19/2011 10.8* Form of Performance Stock Unit Grant Notice and Performance Stock Unit Agreement. 8-K 001-33301 99.2 09/02/2014 10.9* Form of Restricted Stock Unit Grant Notice and Restricted Stock Unit Agreement. 8-K 001-33301 99.1 09/02/2014 10.10* Form of Stock Option Grant Notice and Stock Option Agreement. 8-K 001-33301 99.3 11/23/2011 10.11* Form of 2016 Market Stock Unit Grant Notice and Award Agreement. 8-K 001-33301 99.1 10/02/2015 10.12* Accuray Incorporated Amended and Restated 2016 Equity Incentive Plan and forms of award agreements thereunder. 8-K 001-33301 10.1 11/15/2023 10.13* Amended and Restated 2007 Employee Stock Purchase Plan. 8-K 001-33301 10.2 11/16/2022 10.14* Accuray Incorporated Company Bonus Plan . 10-Q 001-33301 10.6 11/06/2018 10.15* Form of Accuray Incorporated Stand-Alone Inducement Restricted Stock Unit Agreement for Suzanne Winter. S-8 333-234412 99.1 10/31/2019 10.16* Form of Accuray Incorporated Stand-Alone Inducement Stock Option Agreement for Suzanne Winter. S-8 333-234412 99.2 10/31/2019 10.17* Form of Accuray Incorporated Stand-Alone Inducement Restricted Stock Unit Agreement for Jim Dennison . S-8 333-251038 99.4 11/30/2021 10.18* Form of Accuray Incorporated Stand-Alone Inducement Stock Option Agreement for Jim Dennison . S-8 333-251038 99.5 11/30/2021 95 Table of Contents Incorporated by Reference Exhibit No. Exhibit Description Form File No. Exhibit Filing Date Furnished or Filed Herewith 10.19* Form of Accuray Incorporated Stand-Alone Inducement Restricted Stock Unit Agreement for Sandeep Chalke. S-8 333-265330 99.1 05/31/2022 10.20* Form of Accuray Incorporated Stand-Alone Inducement Stock Option Agreement for Sandeep Chalke. S-8 333-265330 99.2 05/31/2022 10.21* TomoTherapy Incorporated 2000 Stock Option Plan, as amended, and forms of option agreements thereunder. S-8 333-174952 99.1 06/17/2011 10.22* TomoTherapy Incorporated 2002 Stock Option Plan, as amended, and forms of option agreements thereunder. S-8 333-174952 99.2 06/17/2011 10.23* TomoTherapy Incorporated 2007 Equity Incentive Plan, as amended, and forms of option agreements thereunder. S-8 333-174952 99.3 06/17/2011 10.24* Form of Indemnification Agreement by and between Registrant and each of its directors and executive officers. 10-Q 001-33301 10.7 05/10/2011 10.25* Executive Employment Agreement by and Between Registrant and Jesse Chew, dated February 3, 2025. 10-Q 001-33301 10.5 02/05/2025 10.26* Executive Employment Agreement by and Between Registrant and Suzanne Winter, dated February 3, 2025 10-Q 001-33301 10.2 02/05/2025 10.27* Executive Employment Agreement by and between Registrant and Leonel Peralta, dated February 3,2025. 10-Q 001-33301 10.1 05/02/2025 10.28* Executive Employment Agreement by and between Registrant and Ali Pervaiz, dated February 3, 2025. 10-Q 001-33301 10.3 02/05/2025 10.29* Executive Employment Agreement by and between Registrant and Sandeep Chalke, dated February 3, 2025. 10-Q 001-33301 10.4 02/05/2025 10.30* Letter Agreement for Interim CEO Role by and between Registrant and Sandeep Chalke, dated September 3, 2024. 10-K 001-33301 10.30 08/28/2025 10.31* Separation Agreement and General Release by and between Registrant and Michael Hoge, dated January 6, 2025 10-Q 001-33301 10.1 02/05/2025 10.32 Form of Exchange Agreement 8-K 001-33301 10.1 06/06/2025 10.33 Governance Agreement, dated as of June 6, 2025, between the Registrant and TCW Asset Management Company LLC 8-K 001-33301 10.2 06/06/2025 10.34 Financing Agreement, dated as of June 6, 2025, between the Registrant as the Administrative Borrower, the guarantors listed hereto, the lenders from time to time party hereto, as lenders, TCW Asset Management Company LLC, as collateral agent and administrative agent, and Wingspire Capital LLC, as servicing agent 10-K 001-33301 10.34 08/28/2025 10.35 Form of Subscription Agreement, dated as of May 6, 2021, between the Registrant and each signatory thereto . 8-K 001-33301 10.2 05/12/2021 96 Table of Contents Incorporated by Reference Exhibit No. Exhibit Description Form File No. Exhibit Filing Date Furnished or Filed Herewith 19.1 Insider Trading Policy 10-K 001-33301 19.1 08/28/2025 21.1 List of subsidiaries. 10-K 001-33301 21.1 08/28/2025 23.1 Consent of Grant Thornton LLP, independent registered public accounting firm. X 31.1 Certification of Chief Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. X 31.2 Certification of Chief Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. X 32.1 Certification of Chief Executive Officer and Chief Financial Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. X 97.1 Compensation Recovery Policy 10-K 001-33301 97.1 08/28/2025 101.INS Inline XBRL Instance Document—the instance document does not appear in the Interactive Data File as its XBRL tags are embedded within the Inline XBRL document X 101.SCH Inline XBRL Taxonomy Extension Schema Document X 101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document X 101.DEF Inline XBRL Taxonomy Extension Definition Linkbase Document X 101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document X 101.PRE Inline XBRL Taxonomy Extension Presentation Linkbase Document X 104 Cover Page Interactive Data File (formatted as inline XBRL and contained in Exhibit 101) * Management contract or compensatory plan or arrangement. † Certain portions of this exhibit have been omitted because they are both not material and would be competitively harmful if publicly disclosed. The certification attached as Exhibit 32.1 that accompanies this Annual Report on Form 10K is not deemed filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of Accuray Incorporated under the Securities Act of 1933 or the Securities Exchange Act of 1934, whether made before or after the date of this Annual Report on Form 10K, irrespective of any general incorporation language contained in such filing. Form 10K, irrespective of any general incorporation language contained in such filing. Item 16. FORM 10-K SUMMARY None. 97 Table of Contents SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of Madison, State of Wisconsin, on February 17, 2026. ACCURAY INCORPORATED By: /s/ STEVE La Neve Steve La Neve President and Chief Executive Officer By: /s/ Ali Pervaiz Ali Pervaiz Senior Vice President and Chief Financial Officer 98 Table of Contents Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following and on the dates indicated. Signature Title Date /s/ Steve La Neve President, Chief Executive Officer and Director (Principal Executive Officer) February 17, 2026 Steve La Neve /s/ Ali Pervaiz Senior Vice President and Chief Financial Officer (Principal Financial Officer) February 17, 2026 Ali Pervaiz * Corporate Controller (Principal Accounting Officer) February 17, 2026 Michael J. Murphy * Chairperson of the Board and Director February 17, 2026 Joseph E. Whitters Director Chan W. Galbato * Director February 17, 2026 Beverly A. Huss * Director February 17, 2026 Anne B. Le Grand * Director February 17, 2026 James M. Hindman * Director February 17, 2026 Mika Nishimura * Director February 17, 2026 Steven F. Mayer * The undersigned, by signing his name hereto, does hereby sign this Amendment No. 1 to Form 10-K/A on behalf of the above indicated officer or director of the registrant, Accuray Incorporated, pursuant to the Power of Attorney signed by such officer or director on August 28, 2025, in the Original Filing. By: /s/ Ali Pervaiz Name: Ali Pervaiz Title: Senior Vice President and Chief Financial Officer Date: February 17, 2026 99