AtlasClear Holdings, Inc.

As filed with the Securities and Exchange Commission on November 7, 2025

No. 333-

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM****S-1

REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933

ATLASCLEAR HOLDINGS, INC.

(Exact name of registrant as specified in its charter)

2203 Lois Ave. Ste. 814

Tampa, FL 33607

(727) 446-6660

(Address, including zip code, and telephone number, including area code, of registrant’s principal executive offices)

John Schaible

Executive Chairman

AtlasClear Holdings, Inc.

2203 Lois Ave., Ste. 814

Tampa, FL 33607

(727) 446-6660

(Name, address, including zip code, and telephone number, including area code, of agent for service)

Copies of all communications, including communications sent to agent for service, should be sent to:

Jason Simon, Esq.

Tricia Branker, Esq.

Greenberg Traurig, LLP

1750 Tysons Boulevard, Suite 1000

McLean, VA 22102

Tel: (703) 749-1300

Approximate date of commencement of proposed sale to the public:

From time to time after this registration statement becomes effective

If any of the securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, check the following box:☒

If this Form is filed to registered additional securities for an offering pursuant to Rule 462(b) under the Securities Act, please check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.☐

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.☐

If this Form is a post-effective amendment filed pursuant to Rule 462(d) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 7(a)(2)(B) of the Securities Act☐

This Registration Statement shall hereafter become effective in accordance with the provisions of Section 8(a) of the Securities Act of 1933.

The information in this preliminary prospectus is not complete and may be changed. These securities may not be sold until the registration statement filed with the Securities and Exchange Commission is effective. The preliminary prospectus is not an offer to sell these securities and does not constitute the solicitation of offers to buy these securities in any jurisdiction where the offer or sale is not permitted.

PRELIMINARY PROSPECTUS

SUBJECT TO COMPLETION, DATED NOVEMBER 7, 2025

ATLASCLEAR HOLDINGS, INC.

Up to 48,597,042 shares of Common Stock by the Selling Stockholders

This prospectus relates to the offer and sale from time to time by the Selling Stockholders named in this prospectus (the “Selling Stockholders”) of an aggregate of up to 48,597,042 shares of our Common Stock, par value $0.0001 per share (“Common Stock”) consisting of:

The shares of Common Stock that may be sold by the Selling Stockholders are collectively referred to in this prospectus as the “Offered Shares.” Our registration of the resale of the Offered Shares does not mean that the Selling Stockholders will offer or sell any of the Offered Shares.

We will not receive any of the proceeds from the sale by the Selling Stockholders of any of the Offered Shares. We will bear all costs, expenses and fees in connection with the registration of the resale of the Offered Shares. The Selling Stockholders will bear all commissions and discounts, if any, attributable to their respective sales of the Offered Shares.

The Selling Stockholders may offer and sell the securities covered by this prospectus in a number of different ways and at varying prices. We provide more information about how the Selling Stockholders may sell the securities in the section titled “Plan of Distribution.”

As of November 7, 2025, the number of shares of Common Stock that may be offered for resale by the Selling Stockholders pursuant to this prospectus is approximately 33.6% of the number of outstanding shares of Common Stock as of November 6, 2025. A significant portion of the shares of our Common Stock being registered for resale may be acquired by Selling Stockholders at prices below the current market price of our Common Stock. This discrepancy in purchase prices may have an impact on the market perception of our Common Stock’s value and could increase the volatility of the market price of our Common Stock or result in a significant decline in the public trading price of our Common Stock. The registration of these shares for resale creates the possibility of a significant increase in the supply of our Common Stock in the market. The increased supply, coupled with the potential disparity in purchase prices, may lead to heightened selling pressure, which could negatively affect the public trading price of our Common Stock. We will not receive any proceeds from the resale of Common Stock by the Selling Stockholders pursuant to this prospectus.

You should carefully read this prospectus, and any applicable prospectus supplement, before you invest in any of our securities.

The shares of Common Stock are listed on the NYSE American LLC (the “NYSE”) under the symbol “ATCH”. On November 5, 2025, the last sale price of the Common Stock as reported on the NYSE was $0.33 per share.

Investing in our securities involves certain risks, including those that are described in the section titled “Risk Factors” beginning on page15** of this prospectus.**

Neither the Securities and Exchange Commission (the “SEC”) nor any state securities commission has approved or disapproved of these securities or determined if this prospectus is truthful or complete. Any representation to the contrary is a criminal offense.

The date of this prospectus is November , 2025.