Rafael Holdings, Inc.

Evaluation of Disclosure Controls and Procedures

An evaluation was performed under the supervision and with the participation of the Company’s management, including the Chief Executive Officer and Chief Financial Officer, of the effectiveness of the design and operation of the Company’s disclosure controls and procedures (as defined in Rule 13a-15(e) promulgated under the Securities Exchange Act of 1934, as amended) as of July 31, 2026. Based on that evaluation, the Company’s management, including the Chief Executive Officer and Chief Financial Officer, concluded that the Company did not maintain effective disclosure controls and procedures because of the material weakness in internal control over financial reporting described below.

Management’s Annual Report on Internal Control over Financial Reporting

The Company’s management is responsible for establishing and maintaining adequate internal control over financial reporting. The internal control process has been designed under management’s supervision to provide reasonable assurance regarding the reliability of financial reporting and the preparation of the Company’s financial statements for external reporting purposes in accordance with U.S. GAAP.

During the year ended July 31, 2025, manage ment identified a material weakness in internal control over financial reporting related to the completeness and accuracy of accruals and associated expenses at Cyclo, a wholly-owned subsidiary. Specifically, controls were not appropriately designed or operating effectively to ensure accruals and related expenses were recorded completely and accurately, due to inadequately designed controls surrounding the month-end accrual identification, measurement, and recognition process, including controls related to clinical trials. The material weakness resulted in immaterial misstatements, which were corrected in the Company’s consolidated financial statements during the year ended July 31, 2025.

Management conducted an assessment of the effectiveness of the Company’s internal control over financial reporting as of July 31, 2026 utilizing the framework established inInternal Control - Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO).

A material weakness is a deficiency, or combination of deficiencies, in internal controls 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.

Because the material weakness identified during the year ended July 31, 2025 had not been remediated as of July 31, 2026, management concluded that the Company’s internal control over financial reporting was not effective as of July 31, 2026.

The Company’s internal control over financial reporting includes policies and procedures that pertain to the maintenance of records that accurately and fairly reflect, in reasonable detail, transactions and dispositions of assets; and provide reasonable assurances that: (1) transactions are recorded as necessary to permit preparation of financial statements in accordance with U.S. GAAP; (2) receipts and expenditures are being made only in accordance with authorizations of management and the directors of the Company; and (3) unauthorized acquisition, use, or disposition of the Company’s assets that could have a material effect on the Company’s financial statements are prevented or timely detected.

All internal control systems, no matter how well designed, have inherent limitations. Therefore, even those systems determined to be effective can provide only reasonable assurance with respect to financial statement preparation and presentation. 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.

This Annual Report on Form 10-K does not include an attestation report of the Company’s registered public accounting firm regarding internal control over financial reporting. Management’s report was not subject to attestation by the Company’s registered public accounting firm pursuant to rules of the Securities and Exchange Commission that permit the Company to provide only management’s report in this Annual Report.

Remediation Plan for Material Weakness in Internal Control Over Financial Reporting

In response to the material weakness identified above, the Company developed a plan, which will be updated as deemed necessary, to remediate the material weakness at Cyclo, including enhancing the design of and implementing additional process-level control activities and ensuring they are properly evidenced and operating effectively. Such design and implementation control activities include, but are not limited to:

Because the reliability of the internal control process requires repeatable execution, the successful on-going remediation of the material weakness will require on-going review and evidence of effectiveness prior to concluding that the controls are effective. Management has not yet completed testing of the operating effectiveness of the new and enhanced controls over a sufficient period of time. The Company’s remediation efforts are underway; however, there is no assurance that the remediation efforts will be effective in the future or that additional material weaknesses will not develop or be identified.

Changes in Internal Control over Financial Reporting

During the quarter ended July 31, 2026, the Company continued to implement the remediation plan described above, including integrating Cyclo’s vendor and accounts payable management process and accrual process into the Company’s existing control process and developing Cyclo’s analytical review and clinical trial accrual estimation processes. These changes have materially affected, or are reasonably likely to materially affect, the Company’s internal control over financial reporting. The material weakness had not been remediated as of July 31, 2026.

Except as described above, there were no changes in the Company’s internal control over financial reporting during the quarter ended July 31, 2026 that have materially affected, or are reasonably likely to materially affect, the Company’s internal control over financial reporting.