AtlasClear Holdings, Inc.

Disclosure Controls and Procedures

Disclosure controls are procedures that are designed with the objective of ensuring that information required to be disclosed in our reports filed under the Exchange Act is recorded, processed, summarized, and reported within the time period specified in the SEC’s rules and forms. Disclosure controls are also designed with the objective of ensuring that such information is accumulated and communicated to our management, including the chief executive officer and chief financial officer, as appropriate to allow timely decisions regarding required disclosure.

Our management, with the participation of our Executive Chairman and Chief Financial Officer, evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act) as of June 30, 2026. Based on that evaluation, and as a result of the remediation of the material weakness in our internal control over financial reporting described below, our Chief Executive Officer and Chief Financial Officer concluded that our disclosure controls and procedures were effective as of June 30, 2026 at a reasonable assurance level.

Management’s Annual Report on Internal Control Over Financial Reporting

As required by SEC rules and regulations implementing Section 404 of the Sarbanes-Oxley Act, our management is responsible for establishing and maintaining adequate internal control over financial reporting. Our internal control over financial reporting is designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of our financial statements for external reporting purposes in accordance with GAAP. Our internal control over financial reporting includes those policies and procedures that:

Because of its inherent limitations, internal control over financial reporting may not prevent or detect errors or misstatements in our financial statements. 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 or compliance with the policies or procedures may deteriorate. Management assessed the effectiveness of our internal control over financial reporting at June 30, 2026. In making these assessments, management used the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission (COSO) in Internal Control — Integrated Framework (2013). Based on our assessments and those criteria, management determined that our internal control over financial reporting was effective as of June 30, 2026.

Remediation of Previously Reported Material Weakness

As previously disclosed in our Annual Report on Form 10-K for the fiscal year ended June 30, 2025, management identified a material weakness in our internal control over financial reporting relating to the technical review and disclosures surrounding complex financial instruments, merger agreements, and related going concern assessments.

During the fiscal year ended June 30, 2026, management implemented a formal remediation plan to enhance our internal controls over accounting for complex transactions. Specifically, management:

1. Enhanced Management Oversight and Review Procedures: Established formal, standardized control activities requiring timely, pre-closing accounting evaluation and documentation for all complex, non-routine, and equity-linked financial transactions.

2. Engagement of Independent Technical Specialists: Implemented a formal control requiring the retention and direct engagement of qualified external third-party technical accounting advisors to assist management in evaluating, accounting for, and reviewing disclosure requirements for complex financial instruments and structural transaction terms.

3. Expanded Technical Accounting Resources: Enhanced access to authoritative GAAP accounting literature and technical research tools, and strengthened internal review protocols prior to financial statement authorization.

Attestation Report of the Registered Public Accounting Firm

This Annual Report does not include an attestation report of our independent registered public accounting firm due to our status as non-accelerated filer under the JOBS Act.

Changes in Internal Control Over Financial Reporting

Except for the remediation controls and enhancements described above implemented during the fiscal year ended June 30, 2026, there were no changes in our internal control over financial reporting that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting during the quarter ended June 30, 2026.