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

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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.

Interest in Securities of the Issuer.

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.