<PAGE>
 
                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C.  20549

                                  FORM 10-Q/A

                                Amendment No. 1
                                        


[X]  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE
     ACT OF 1934

     For the quarterly period ended   December 31, 1998
                                      -----------------

                                       OR

[ ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
     EXCHANGE ACT OF 1934


     Commission file number        1-14224
                                 ------------


                                Paymentech, Inc.
--------------------------------------------------------------------------------
             (Exact Name of Registrant as Specified in its Charter)


            Delaware                                    75-2634185
--------------------------------------------------------------------------------
(State or other jurisdiction of                      (I.R.S. Employer
 incorporation or organization)                    Identification Number)


1601 Elm Street, 9th Floor, Dallas, Texas                       75201
--------------------------------------------------------------------------------
(address of principal executive offices)                      (Zip Code)


Registrant's Telephone Number, including area code   214-849-2149
                                                     ------------

                                      N/A
--------------------------------------------------------------------------------
Former Name, Former Address and former Fiscal Year, If Changed Since Last Report


Indicate by check mark whether the registrant (1) has filed all reports required
to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during
the preceding 12 months (or for such shorter period that the registrant was
required to file such reports), and (2) has been subject to such filing
requirements for the past 90 days.  Yes    X     No   
                                        -------     -------   


Indicate the number of shares outstanding of each of the issuer's classes of
common stock, as of the latest practicable date.

              Class                           Outstanding at March 31, 1999
---------------------------------------    -------------------------------------
    Common Stock, $.01 par value                     36,380,874 shares
<PAGE>
                               EXPLANATORY NOTE

    Paymentech, Inc. (the "Company") has requested confidential treatment with
respect to portions of Exhibit 2.1 to the Form 10-Q. This amendment is being
filed to reflect changes to Exhibit 2.1 as per the Securities and Exchange
Commission's staff's comments to the Company's request for confidential
treatment. Certain previously redacted information has been added back into
Exhibit 2.1 of this amended filing. No other changes are made to the Form 10-Q
as originally filed.

PART II.  OTHER INFORMATION
 
Item 6.    Exhibits and Reports on Form 8-K

a.  Reports on Form 8-K filed during the second quarter of fiscal 1999:

          Report on Form 8-K filed October 29, 1998
                  Item 5.  Other Events
                  Exhibit 99.  Press Release
 
          Report on Form 8-K filed December 28, 1998
                  Item 5.  Other Events
                  Exhibit 99.  Press Release
 
b.  Reports on Form 8-K filed subsequent to the second quarter of fiscal 1999:

          Report on Form 8-K filed February 17, 1999
                  Item 5.  Other Events
                  Item 7.  Financial Statements and Exhibits

          Report on Form 8-K filed March 23, 1999
                  Item 5.  Other Events
                  Item 7.  Financial Statements, Pro Forma
                           Financial Information and Exhibits
 
c.  Exhibits

    The following exhibits are incorporated by reference or filed herewith:

Exhibit Number  Description of Exhibit
--------------  ----------------------
      2.1*      Merchant Asset Purchase Agreement, dated as of October 28, 1998
                by and between Mellon Bank, N.A., as Seller, and Paymentech
                Management Resources, Inc., as Purchaser. (Confidential
                treatment has been requested for portions of this exhibit and,
                accordingly, such portions have been omitted from the exhibit.
                The entire document, including the portions omitted from the
                exhibit, have been provided separately to the Commission).

      27**      Financial Data Schedule.

------------------------ 
 * Filed herewith.
** Exhibit originally filed with the Registrant's Form 10-Q on February 16, 1999
   and is not affected by this Form 10-Q/A.




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<PAGE>
 
                                   SIGNATURES
                                        

  Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.


  Date:   April 8, 1999


                            Paymentech, Inc.



                            By: /s/ Pamela H. Patsley
                                -----------------------------------------
                                Pamela H. Patsley
                                President and Chief Executive Officer



                            By: /s/ Kathryn J. Kessler
                                -----------------------------------------
                                Kathryn J. Kessler
                                Chief Financial Officer







 

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<PAGE>
 
                               INDEX OF EXHIBITS
                               -----------------
                                        


                                                        Sequentially
Exhibit Number             Description of Exhibit      Numbered Page
--------------             ----------------------      -------------

     2.1*          Merchant Asset Purchase Agreement, dated as of October 28,
                   1998 by and between Mellon Bank, N.A., as Seller, and
                   Paymentech Management Resources, Inc., as Purchaser.
                   (Confidential treatment has been requested for portions of
                   this exhibit and, accordingly, such portions have been
                   omitted from the exhibit. The entire document, including the
                   portions omitted from the exhibit, have been provided
                   separately to the Commission).

    27**           Financial Data Schedule.
--------------
 * Filed herewith.
** Exhibit originally filed with the Registrant's Form 10-Q on February 16, 1999
   and is not affected by this Form 10-Q/A.




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