13D Filing: Flexpoint Fund Ii, L.p. and Jetpay Corp (NASDAQ:JTPY)

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)

JetPay
Corporation

(Name of Issuer)

Common Stock

(Title of
Class of Securities)

913384103

(CUSIP Number)

Charles
E. Glew

Steven M. Michienzi

Flexpoint Fund II, L.P.

Flexpoint Ford, LLC

676
N. Michigan Ave., Suite 3300

Chicago, Illinois 60611

(312) 327-4525

Copy
to:

James S. Rowe

Mark A. Fennell, P.C.

Kirkland & Ellis LLP

300 North LaSalle

Chicago, Illinois 60654

(312) 862-2000

(Name,
Address and Telephone Number of Person Authorized to Receive Notices and Communications)

March 22, 2017

(Date of Event Which Requires Filing of this Statement)

If the filing person has
previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box.
☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See §240.13d-7 for
other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be
deemed to be filed for the purpose of Section 18 of the Securities Exchange Act of 1934 (Act) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act
(however, see the Notes).

This Amendment No. 2 (this Amendment) amends and supplements the Statement on
Schedule 13D filed with the Securities and Exchange Commission (the Commission) on October 21, 2013, as amended by Amendment No. 1 filed with the Commission on October 24, 2016 (the Schedule 13D) by Flexpoint
Fund II, L.P. (the Investor), Flexpoint Management II, L.P. (Flexpoint Management), Flexpoint Ultimate Management II, LLC (Flexpoint Ultimate) and Donald J. Edwards (Edwards). The Schedule 13D relates
to shares of common stock, par value $0.001 (Common Stock) of JetPay Corporation, a Delaware corporation (Issuer), issuable upon conversion of shares of series A preferred stock, par value $0.001 per share (Series A
Preferred Stock). Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to such terms in the Schedule 13D. Except as otherwise provided herein, all Items of the Schedule 13D remain unchanged.

Item 5 is hereby amended and restated in its
entirety to read as follows:

(a), (b)

The information contained on the cover pages to this Schedule 13D and the information set forth or incorporated in Items 2, 3, 4 and 6 hereof
are incorporated herein by reference.

As of March 29, 2017, the Investor is the record owner of 99,666 shares of Series A Preferred
Stock, which are convertible at the current conversion price of $2.36 into approximately 12,669,407 shares of Common Stock, representing approximately 44.8% of the outstanding Common Stock, based on 15,588,984 shares of Common Stock outstanding as
of March 21, 2017, plus an additional 12,669,407 shares of Common Stock issuable upon conversion of the Series A Preferred Stock. Due to their relationship with the Investor, Flexpoint Management, Flexpoint Ultimate, and Edwards may be deemed
to have shared voting power with respect to the Series A Preferred Stock beneficially owned by the Investor, and as a result, Flexpoint Management, Flexpoint Ultimate, and Edwards may be deemed to have shared beneficial ownership of such shares of
Series A Preferred Stock.

Under the definition of beneficial ownership as set forth in Rule
13d-3 under the Exchange Act, as a result of the entry into the A&R Purchase Agreement, the Reporting Persons may be deemed to be members of a group with Sundara and, as a result, to
beneficially own the 33,667 shares of Series A Preferred Stock acquired by Sundara pursuant to the A&R Purchase Agreement and the Underlying Shares into which they may be converted. As described in Item 4 above and for the reasons stated
therein, the Reporting Persons disclaim beneficial ownership of all such securities.

Although the Reporting Persons disclaim beneficial
ownership of the 33,667 shares owned by Sundara, if such shares were aggregated with the 99,666 shares of Series A Preferred Stock beneficially owned by the Reporting Persons, the Reporting Persons would be deemed to beneficially own 133,333 shares
of Series A Preferred Stock, convertible into 16,949,110 shares of Common Stock, constituting approximately 52.1% of the outstanding shares of Common Stock.

Except as set forth above, neither any Reporting Person nor, to the best of the Reporting Persons knowledge, Sundara, owns any shares of
Common Stock.

Neither the filing of this Statement nor any of its contents shall be deemed to constitute an admission that any Reporting
Person is the beneficial owner of the Series A Preferred Stock or the Common Stock referred to herein for purposes of Section 13(d) of the Exchange Act or for any other purpose, and such beneficial ownership is expressly disclaimed.

(c)

Except as set forth
in this Item 5, none of the Reporting Persons has engaged in any transaction during the past 60 days involving shares of Common Stock or Series A Preferred Stock.

(d), (e)

Not applicable.

Item 6 is hereby amended to add the following disclosure under the heading Amended and Restated Purchase Agreement in such Item:

On November 16, 2016, the Investor made an indemnification claim against the Company pursuant to the A&R Purchase Agreement (the
Second Direct Air Indemnification Claim). As a result of the Second Direct Air Indemnification Claim, the Conversion Price applicable to the Series A Preferred Stock was adjusted to $2.36 on March 22, 2017, in accordance with the
terms of the A&R Purchase Agreement and the Certificate of Designation governing the Series A Preferred Stock.

Signatures

After reasonable inquiry and to the best knowledge and belief of the undersigned, such person certifies that the information set forth in this Amendment with
respect to such person is true, complete and correct.