Tonix Pharmaceuticals Holding Corp.

Management’s evaluation of disclosure controls and procedures

Our management, with the participation of our Chief Executive Officer and Chief Financial Officer, evaluated the effectiveness of our disclosure controls and procedures pursuant to Rule 13a-15 under the Exchange Act. In designing and evaluating the disclosure controls and procedures, management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives. In addition, the design of disclosure controls and procedures must reflect the fact that there are resource constraints, and that management is required to apply its judgment in evaluating the benefits of possible controls and procedures relative to their costs.

Based on management’s evaluation, our Chief Executive Officer and Chief Financial Officer concluded that our disclosure controls and procedures are designed at a reasonable assurance level and are effective to provide reasonable assurance that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in SEC 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.

Management’s report on internal control over financial reporting.

Our management is responsible for establishing and maintaining adequate internal control over financial reporting for our company. Internal control over financial reporting is defined in Rule 13a-15(f) and 15d-15(f) promulgated under the Exchange Act, as a process designed by, or under the supervision of, a company’s principal executive and principal financial officer and effected by the our board of directors, management and other personnel, 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 and includes those policies and procedures that:

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. 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. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible enhancements to controls and procedures.

We conducted an evaluation of the effectiveness of internal control over financial reporting based on the framework in Internal Control — Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. Based on this evaluation, our principal executive officer and principal financial officer conclude that, at December 31, 2024, our internal control over financial reporting was effective.

This annual report does not include an attestation report by EisnerAmper LLP, our independent registered public accounting firm regarding internal control over financial reporting. As a smaller reporting company, our management’s report was not subject to attestation by our registered public accounting firm pursuant to rules of the Securities and Exchange Commission that permit us to provide only management’s report in this annual report.

Previously Reported Material Weakness in Internal Control Over Financial Reporting

In the 2024 Form 10-Q, filed with the SEC on August 16, 2024, management concluded that our internal control over financial reporting was not effective as of June 30, 2024. In the evaluation, we did not maintain an effective control environment over the internal control activities to ensure the proper recognition and measurement related to the accounting for complex and non-routine transactions. We did not have adequate supervision and review controls over the complex accounting related to the non-cash impairment of intangibles, non-cash equity transactions and the recoverability of inventory. As a result, management review of asset impairment calculations did not identify errors in the associated cash flow projections which led to an error in the conclusion of the initial impairment assessment. We also did not properly assess the realizability of inventory based upon the projections utilized and our assessment of an amendment to existing warrants that were reclassified into equity in the same period did not include a quantitative evaluation of the potential materiality of revaluation adjustments.

In connection with the material weakness as it relates to the accounting for complex and non-routine transactions related to the non-cash impairment of intangibles, non-cash equity transactions and the recoverability of inventory, management re-evaluated the effectiveness of such controls as of December 31, 2024, and concluded that such controls were remediated and operating effectively as of December 31, 2024. The remediation of the material weakness over the complex accounting related to the non-cash impairment of intangibles, non-cash equity transactions was as a result of no material balances related to these financial statement captions as of December 31, 2024, and consequently there was no risk of material misstatements for these financial statement captions. While there were no material balances for the intangible assets as of December 31, 2024 and no non-cash equity transactions for the period July 1, 2024 to December 31, 2024, management’s testing of internal controls over financial reporting as of December 31, 2024 included controls that were similar in nature to the controls that were not operating effectively as of June 30, 2024 and noted such controls were operating effectively as of December 31, 2024.

In relation to the realizability of inventory, the remediation of this material weakness constituted implementing new controls with expanded review processes including but not limited to the assessment of additional data points for the assessment and additional personnel included to evaluate our ability to realize inventory balances.

Changes in internal control over financial reporting.

Other than as described above, there were no changes in our internal control over financial reporting that occurred during the year ended December 31, 2024 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.