<PAGE>   1
 
                                                                    EXHIBIT 99.1
 
                             LETTER OF TRANSMITTAL
 
                                   TO TENDER
               UNREGISTERED 9% SENIOR SUBORDINATED NOTES DUE 2008
                                       OF
 
                          COOPERATIVE COMPUTING, INC.
   PURSUANT TO THE EXCHANGE OFFER AND PROSPECTUS DATED                , 1998
 
THE EXCHANGE OFFER AND WITHDRAWAL RIGHTS WILL EXPIRE AT 5:00 P.M., NEW YORK CITY
TIME, ON             , 1998 (THE "EXPIRATION DATE"), UNLESS THE EXCHANGE OFFER
IS EXTENDED BY THE COMPANY.
 
                 The Exchange Agent for the Exchange Offer is:
 
                          NORWEST BANK MINNESOTA, N.A.
 
                                   Deliver to
          Norwest Bank Minnesota, National Association, Exchange Agent
 
<TABLE>
<S>                             <C>                             <C>
  By Registered or Certified        By Overnight Courier:             By Hand Delivery:
            Mail:
 Norwest Bank Minnesota, N.A.    Norwest Bank Minnesota, N.A.    Norwest Bank Minnesota, N.A.
  Corporate Trust Operations       Corporate Trust Services        Northstar East Building
        P.O. Box 1517             Sixth and Marquette Avenue       608 Second Avenue South,
  Minneapolis, MN 55480-1517      Minneapolis, MN 55479-0113              12th Floor
                                                                   Corporate Trust Services
                                                                       Minneapolis, MN
</TABLE>
 
                         Facsimile Transmission Number:
 
                        (For Eligible Institutions Only)
                                 (612) 667-4927
 
                   Confirm Receipt of Facsimile by Telephone:
 
                                 (612) 667-9764
 
    (Originals of all documents sent by facsimile should be sent promptly by
                                 registered or
          certified mail, by hand, or by overnight delivery service.)
 
     DELIVERY OF THIS LETTER OF TRANSMITTAL TO AN ADDRESS OR TRANSMISSION OF
INSTRUCTIONS VIA FACSIMILE OTHER THAN AS SET FORTH ABOVE WILL NOT CONSTITUTE A
VALID DELIVERY.
 
     IF YOU WISH TO EXCHANGE UNREGISTERED 9% SENIOR SUBORDINATED NOTES DUE 2008,
FOR AN EQUAL AGGREGATE PRINCIPAL AMOUNT OF REGISTERED 9% SENIOR SUBORDINATED
NOTES DUE 2008, PURSUANT TO THE EXCHANGE OFFER, YOU MUST VALIDLY TENDER (AND NOT
WITHDRAW) OLD NOTES TO THE EXCHANGE AGENT PRIOR TO THE EXPIRATION DATE.
 
                          SIGNATURES MUST BE PROVIDED
 
              PLEASE READ THE ACCOMPANYING INSTRUCTIONS CAREFULLY.
 
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<PAGE>   2
 
                       DESCRIPTION OF TENDERED OLD NOTES
 
<TABLE>
<CAPTION>
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                                                                                        AGGREGATE
                                                                                        PRINCIPAL
      NAME(S) AND ADDRESS(ES) OF REGISTERED OWNER(S)            CERTIFICATE               AMOUNT
AS IT APPEARS ON THE 9% SENIOR SUBORDINATED NOTES DUE 2008       NUMBER(S)             OF OLD NOTES
                (PLEASE FILL IN, IF BLANK)                      OF OLD NOTES             TENDERED
--------------------------------------------------------------------------------------------------------
<S>                                                        <C>                    <C>
                                                           ==========================================
                                                           ==========================================
                                                           TOTAL PRINCIPAL AMOUNT
                                                             OF NOTES TENDERED
--------------------------------------------------------------------------------------------------------
</TABLE>
 
Ladies and Gentlemen:
 
     1. The undersigned hereby tenders to Cooperative Computing, Inc., a
Delaware corporation (the "Company"), the 9% Senior Subordinated Notes due 2008
(the "Old Notes"), described above pursuant to the Company's offer of $1,000
principal amount of 9% Senior Subordinated Notes due 2008 (the "New Notes"), in
exchange for each $1,000 principal amount of the Old Notes, upon the terms and
subject to the conditions contained in the Prospectus dated             , 1998
(the "Prospectus"), receipt of which is hereby acknowledged, and in this Letter
of Transmittal (which together constitute the "Exchange Offer").
 
     2. The undersigned hereby represents and warrants that it has full
authority to tender the Old Notes described above. The undersigned will, upon
request, execute and deliver any additional documents deemed by the Company to
be necessary or desirable to complete the tender of Old Notes.
 
     3. The undersigned understands that the tender of the Old Notes pursuant to
all of the procedures set forth in the Prospectus will constitute an agreement
between the undersigned and the Company as to the terms and conditions set forth
in the Prospectus.
 
     4. Unless the box under the heading "Special Registration Instructions" is
checked, the undersigned hereby represents and warrants that:
 
          (i) the New Notes acquired pursuant to the Exchange Offer are being
     obtained in the ordinary course of business of the undersigned, whether or
     not the undersigned is the holder;
 
          (ii) neither the undersigned nor any such other person is engaging in
     or intends to engage in a distribution of such New Notes;
 
          (iii) neither the undersigned nor any such other person has an
     arrangement or understanding with any person to participate in the
     distribution of such New Notes; and
 
          (iv) neither the holder nor any such other person is an "affiliate,"
     as such term is defined under Rule 405 promulgated under the Securities Act
     of 1933, as amended (the "Securities Act"), of the Company.
 
     5. The undersigned may, IF, AND ONLY IF, UNABLE TO MAKE ALL OF THE
REPRESENTATIONS AND WARRANTIES CONTAINED IN ITEM 4 ABOVE, elect to have its Old
Notes registered in the shelf registration described in the Exchange and
Registration Rights Agreement, dated as of February 10, 1998, between the
Company and the purchasers of the Old Notes in the form filed as an exhibit to
the Registration Statement (the "Registration Agreement") (all terms used in
this Item 5 with their initial letters capitalized, unless otherwise defined
herein, shall have the meanings given them in the Registration Agreement). Such
election may be made by checking the box under "Special
 
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<PAGE>   3
 
   
Registration Instructions" on page 4. By making such election, the undersigned
agrees, as a holder of Transfer Restricted Securities participating in a shelf
registration, to indemnify and hold harmless the Company, its directors and
officers and each person, if any, who controls the Company within the meaning of
either Section 15 of the Securities Act or Section 20 of the Securities Exchange
Act of 1934, as amended (the "Exchange Act"), from and against any loss, claim,
damage or liability (including, without limitation, any legal or other expenses
reasonably incurred in connection with defending or investigating any such
action or claim), joint or several, or any action in respect thereof, to which
the Company or any such director, officer or controlling person may become
subject, under the Securities Act or otherwise, insofar as such loss, claim,
damage, liability or action arises out of, or is based upon (i) any untrue
statement or alleged untrue statement of a material fact contained in the Shelf
Registration Statement or the Prospectus or in any amendment or supplement
thereto, (ii) or the omission or alleged omission to state therein a material
fact required to be stated therein or necessary to make the statements therein
not misleading, but only with reference to such information relating to the
undersigned furnished in writing by or on behalf of the undersigned expressly
for use in the Shelf Registration Statement, the Prospectus or any amendments or
supplements thereto. Any such indemnification shall be governed by the terms and
subject to the conditions set forth in the Registration Agreement, including,
without limitation, the provisions regarding notice, retention of counsel,
contribution and payment of expenses set forth therein. The above summary of the
indemnification provision of the Registration Agreement is not intended to be
exhaustive and is qualified in its entirety by the Registration Agreement.
    
 
     6. If the undersigned is not a broker-dealer, the undersigned represents
that it is not engaged in, and does not intend to engage in, a distribution of
New Notes. If the undersigned is a broker-dealer that will receive New Notes for
its own account in exchange for Old Notes that were acquired as a result of
market-making activities or other trading activities, it acknowledges that it
will deliver a prospectus in connection with any resale of such New Notes;
however, by so acknowledging and delivering a prospectus, the undersigned will
not be deemed to admit that it is an "underwriter" within the meaning of the
Securities Act. If the undersigned is a broker-dealer and Old Notes held for its
own account were not acquired as a result of market-making or other trading
activities, such Old Notes cannot be exchanged pursuant to the Exchange Offer.
 
     7. Any obligation of the undersigned hereunder shall be binding upon the
successors, assigns, executors, administrators, trustees in bankruptcy and legal
and personal representatives of the undersigned.
 
     8. Unless otherwise indicated herein under "Special Delivery Instructions,"
the certificates for the New Notes will be issued in the name of the
undersigned.
 
                         SPECIAL DELIVERY INSTRUCTIONS
                              (SEE INSTRUCTION 1)
 
     To be completed ONLY IF the New Notes are to be issued or sent to someone
other than the undersigned or to the undersigned at an address other than that
provided above.
            Mail [ ] Issue [ ] (check appropriate boxes) certificates to:
 
Name:
     ---------------------------------------------------------------------------
                                 (Please Print)
 
Address:
        ------------------------------------------------------------------------

        ------------------------------------------------------------------------

        ------------------------------------------------------------------------
                              (Including Zip Code)
 
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<PAGE>   4
 
                       SPECIAL REGISTRATION INSTRUCTIONS
                                  (SEE ITEM 5)
 
     To be completed ONLY IF (i) the undersigned satisfies the conditions set
forth in Item 5 above, (ii) the undersigned elects to register its Old Notes in
the shelf registration described in the Registration Agreement, and (iii) the
undersigned agrees to indemnify certain entities and individuals as set forth in
the Registration Agreement and summarized in Item 5 above.
 
     [ ] By checking this box the undersigned hereby (i) represents that it is
unable to make all of the representations and warranties set forth in Item 4
above, (ii) elects to have its Old Notes registered pursuant to the shelf
registration described in the Registration Agreement, and (iii) agrees to
indemnify certain entities and individuals identified in, and to the extent
provided in, the Registration Agreement and summarized in Item 5 above.
 
                       SPECIAL BROKER-DEALER INSTRUCTIONS
                                  (SEE ITEM 6)
 
     [ ] Check here if you are a broker-dealer and wish to receive 10 additional
copies of the Prospectus and 10 copies of any amendments or supplements thereto.
 
Name:
     ---------------------------------------------------------------------------
                                 (Please Print)
 
Address:
        ------------------------------------------------------------------------
 
        ------------------------------------------------------------------------
 
        ------------------------------------------------------------------------
                              (Including Zip Code)
 
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<PAGE>   5
 
                                   SIGNATURE
 
     To be completed by all exchanging noteholders. Must be signed by registered
holder exactly as name appears on Old Notes. If signature is by trustee,
executor, administrator, guardian, attorney-in-fact, officer of a corporation or
other person acting in a fiduciary or representative capacity, please set forth
full title. See Instruction 3.
 
X
--------------------------------------------------------------------------------
 
X
--------------------------------------------------------------------------------
           Signature(s) of Registered Holder(s) Authorized Signature
 
Dated:
--------------------------------------------------------------------------------
 
Name(s):
--------------------------------------------------------------------------------
 
--------------------------------------------------------------------------------
                             (Please Type or Print)
 
Capacity:
--------------------------------------------------------------------------------
 
Address:
--------------------------------------------------------------------------------
 
--------------------------------------------------------------------------------
 
--------------------------------------------------------------------------------
                              (Including Zip Code)
 
Area Code and Telephone Number:
-----------------------------------------------------------------------
 
               SIGNATURE GUARANTEE (IF REQUIRED BY INSTRUCTION 1)
 
        Certain Signatures Must be Guaranteed by an Eligible Institution
 
--------------------------------------------------------------------------------
             (Name of Eligible Institution Guaranteeing Signatures)
 
--------------------------------------------------------------------------------
  (Address (including zip code) and Telephone Number (including area code) of
                                     Firm)
 
--------------------------------------------------------------------------------
                             (Authorized Signature)
 
--------------------------------------------------------------------------------
                                 (Printed Name)
 
--------------------------------------------------------------------------------
                                    (Title)
 
Dated:
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                      PLEASE READ THE INSTRUCTIONS BELOW,
                WHICH FORM A PART OF THIS LETTER OF TRANSMITTAL.
 
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<PAGE>   6
 
                                  INSTRUCTIONS
 
     1. GUARANTEE OF SIGNATURES. Signatures on this Letter of Transmittal must
be guaranteed by an eligible guarantor institution that is a member of or
participant in the Securities Transfer Agents Medallion Program, the New York
Stock Exchange Medallion Signature Program, the Stock Exchange Medallion
Program, or by an "eligible guarantor institution" within the meaning of Rule
17Ad-15 promulgated under the Exchange Act (an "Eligible Institution") unless
the box entitled "Special Registration Instructions" or "Special Delivery
Instructions" above has not been completed or the Old Notes described above are
tendered for the account of an Eligible Institution.
 
     2. DELIVERY OF LETTER OF TRANSMITTAL AND OLD NOTES. The Old Notes, together
with a properly completed and duly executed Letter of Transmittal (or copy
thereof), should be mailed or delivered to the Exchange Agent at the address set
forth above.
 
     THE METHOD OF DELIVERY OF OLD NOTES AND THE LETTER OF TRANSMITTAL AND ALL
OTHER REQUIRED DOCUMENTS TO THE EXCHANGE AGENT IS AT THE ELECTION AND RISK OF
THE HOLDER. INSTEAD OF DELIVERY BY MAIL, IT IS RECOMMENDED THAT HOLDERS USE AN
OVERNIGHT OR HAND DELIVERY SERVICE. IN ALL CASES, SUFFICIENT TIME SHOULD BE
ALLOWED TO ASSURE DELIVERY TO THE EXCHANGE AGENT BEFORE THE EXPIRATION DATE. NO
LETTER OF TRANSMITTAL OR OLD NOTES SHOULD BE SENT TO THE COMPANY. HOLDERS MAY
REQUEST THEIR RESPECTIVE BROKERS, DEALERS, COMMERCIAL BANKS, TRUST COMPANIES, OR
NOMINEES TO EFFECT THE ABOVE TRANSACTIONS FOR SUCH HOLDERS.
 
     3. SIGNATURE ON LETTER OF TRANSMITTAL, BOND POWERS AND ENDORSEMENTS. If
this Letter of Transmittal is signed by a person other than a registered holder
of any Old Notes, such Old Notes must be endorsed or accompanied by appropriate
bond powers, signed by such registered holder exactly as such registered
holder's name appears on such Old Notes.
 
     If this Letter of Transmittal or any Old Notes or bond powers are signed by
trustees, executors, administrators, guardians, attorneys-in-fact, officers of
corporations, or others acting in a fiduciary or representative capacity, such
persons should so indicate when signing, and, unless waived by the Company,
proper evidence satisfactory to the Company of their authority to so act must be
submitted with this Letter of Transmittal.
 
     4. MISCELLANEOUS. All questions as to the validity, form, eligibility
(including time of receipt), acceptance, and withdrawal of tendered Old Notes
will be determined by the Company in its sole discretion, which determination
will be final and binding on all parties. The Company reserves the absolute
right to reject any or all Old Notes not properly tendered or any Old Notes the
Company's acceptance of which would, in the opinion of counsel for the Company,
be unlawful. The Company also reserves the right to waive any defects,
irregularities, or conditions of tender as to particular Old Notes. The
Company's interpretation of the terms and conditions of the Exchange Offer
(including the instructions in this Letter of Transmittal) will be final and
binding. Unless waived, any defects or irregularities in connection with tenders
of Old Notes must be cured within such time as the Company shall determine.
Neither the Company, the Exchange Agent, nor any other person shall be under any
duty to give notification of defects in such tenders or shall incur any
liability for failure to give such notification. Tenders of Old Notes will not
be deemed to have been made until such defects or irregularities have been cured
or waived. Any Old Notes received by the Exchange Agent that are not properly
tendered and as to which the defects or irregularities have not been cured or
waived will be returned by the Exchange Agent to the tendering holder thereof as
soon as practicable following the Expiration Date.
 
                                        6