<PAGE>

                                                                     EXHIBIT 4.2

         NEITHER THE WARRANTS REPRESENTED BY THIS WARRANT CERTIFICATE NOR THE
SHARES OF COMMON STOCK, PAR VALUE $.001 PER SHARE, OF AIRTRAN HOLDINGS, INC. FOR
WHICH THE WARRANT IS EXERCISABLE HAVE BEEN REGISTERED UNDER THE SECURITIES ACT
OF 1933, AS AMENDED (THE "SECURITIES ACT"), OR ANY STATE SECURITIES LAWS.
NEITHER THIS WARRANT CERTIFICATE NOR ANY INTEREST OR PARTICIPATION HEREIN NOR
ANY SHARE OF COMMON STOCK ACQUIRED UPON EXERCISE HEREOF MAY BE OFFERED, SOLD,
ASSIGNED, TRANSFERRED, PLEDGED, ENCUMBERED OR OTHERWISE DISPOSED OF IN THE
ABSENCE OF SUCH REGISTRATION OR UNLESS SUCH TRANSACTION IS EXEMPT FROM, OR NOT
SUBJECT TO, REGISTRATION.

         THE HOLDER OF THE WARRANTS REPRESENTED BY THIS WARRANT CERTIFICATE OR
ANY SECURITIES OF THE COMPANY FOR WHICH THE WARRANT IS EXERCISABLE, BY ITS
ACCEPTANCE HEREOF, AGREES TO OFFER, SELL OR OTHERWISE TRANSFER THE WARRANTS
REPRESENTED BY THIS WARRANT CERTIFICATE ONLY (A) TO THE COMPANY, (B) PURSUANT TO
A REGISTRATION STATEMENT WHICH HAS BEEN DECLARED EFFECTIVE UNDER THE SECURITIES
ACT, (C) FOR SO LONG AS THE WARRANTS REPRESENTED BY THIS WARRANT CERTIFICATE ARE
ELIGIBLE FOR RESALE PURSUANT TO AN EXEMPTION FROM REGISTRATION UNDER THE
SECURITIES ACT, TO A PERSON IT REASONABLY BELIEVES IS A "QUALIFIED INSTITUTIONAL
BUYER" AS DEFINED IN RULE 144A UNDER THE SECURITIES ACT THAT PURCHASES FOR ITS
OWN ACCOUNT OR FOR THE ACCOUNT OF A QUALIFIED INSTITUTIONAL BUYER TO WHOM NOTICE
IS GIVEN THAT THE TRANSFER IS BEING MADE IN RELIANCE ON AN EXEMPTION FROM
REGISTRATION UNDER THE SECURITIES ACT, (D) PURSUANT TO OFFERS AND SALES TO NON-
U.S. PERSONS THAT OCCUR OUTSIDE THE UNITED STATES WITHIN THE MEANING OF
REGULATION S UNDER THE SECURITIES ACT, (E) TO AN INSTITUTIONAL "ACCREDITED
INVESTOR" WITHIN THE MEANING OF SUBPARAGRAPH (A)(1), (2), (3) OR (7) OF RULE 501
UNDER THE SECURITIES ACT THAT IS ACQUIRING THE WARRANTS REPRESENTED BY THIS
WARRANT CERTIFICATE FOR ITS OWN ACCOUNT, OR FOR THE ACCOUNT OF SUCH AN
INSTITUTIONAL "ACCREDITED INVESTOR," FOR INVESTMENT PURPOSES AND NOT WITH A VIEW
TO, OR FOR OFFER OR SALE IN CONNECTION WITH, ANY DISTRIBUTION IN VIOLATION OF
THE SECURITIES ACT OR (F) PURSUANT TO ANOTHER AVAILABLE EXEMPTION FROM THE
REGISTRATION REQUIREMENTS OF THE SECURITIES ACT, SUBJECT TO THE COMPANY'S AND
THE WARRANT AGENT'S, AS APPLICABLE, RIGHT PRIOR TO ANY SUCH OFFER, SALE OR
TRANSFER PURSUANT TO CLAUSE (D), (E) OR (F) TO REQUIRE THE DELIVERY OF AN
OPINION OF COUNSEL, CERTIFICATION AND/OR OTHER INFORMATION REASONABLY
SATISFACTORY TO EACH OF THEM, AND IN EACH OF THE FOREGOING CASES, AN ASSIGNMENT
IN THE FORM APPEARING ON THE OTHER SIDE OF THIS WARRANT CERTIFICATE IS COMPLETED
AND DELIVERED BY THE TRANSFEROR TO THE WARRANT AGENT. THIS LEGEND SHALL BE
REMOVED UPON THE REQUEST OF A HOLDER AFTER THE RESALE RESTRICTION TERMINATION
DATE.
<PAGE>

         THIS SECURITY IS SUBJECT TO A REGISTRATION RIGHTS AGREEMENT DATED AS OF
APRIL 12, 2001 BETWEEN THE COMPANY AND BOEING CAPITAL LOAN CORPORATION (THE
"INITIAL PURCHASER"), A COPY OF WHICH IS ON FILE WITH THE SECRETARY OF THE
COMPANY.

No. ATH-1                                                       166,400 Warrants
                              WARRANT CERTIFICATE

                            AIRTRAN HOLDINGS, INC.

                  This Warrant Certificate certifies that Boeing Loan
Corporation, or registered assigns, is the registered holder (the "Holder") of
166,400 Warrant(s) (the "WARRANT(S)") to purchase shares of Common Stock, $0.001
par value per share (the "COMMON STOCK"), of AIRTRAN HOLDINGS, INC., a Nevada
corporation (the "COMPANY"). Each Warrant entitles the Holder to purchase from
the Company at any time from 9:00 a.m. New York City time on or after the
Exercisability Date (as defined in the Warrant Agreement) until 5:00 p.m., New
York City time, on April 12, 2006 (the "EXPIRATION DATE"), 18.02885 fully paid
and nonassessable shares of Common Stock (as may be adjusted, the "WARRANT
SHARES", and which may also include any other securities or property purchasable
upon exercise of a Warrant, such adjustment and inclusion each as provided in
the Warrant Agreement) at the exercise price (the "EXERCISE PRICE") of $4.51 per
Warrant Share upon surrender of this Warrant Certificate and payment of the
Exercise Price at any office or agency maintained for that purpose by the
Company (the "WARRANT AGENT OFFICE"), subject to the conditions set forth herein
and in the Warrant Agreement. Notwithstanding the foregoing, in the event that
any Holder of Warrant Certificates delivers such Warrant Certificates to the
Company and indicates on the Election to Exercise that such Holder intends to
exercise all, or any portion of, the Warrants represented by such Warrant
Certificate to satisfy its obligation to pay the Exercise, such Holder shall be
entitled to receive, a number of Warrant Shares in respect of the exercise of
such Warrants equal to the product of: (A) the number of Warrant Shares issuable
                           ----------
upon the exercise of such Warrant Certificates (or, if only a portion of such
Warrant Certificates are being exercised, issuable upon the exercise of such
portion) multiplied by (B) the quotient of: (i) the difference between: (X) the
         -------------         -----------          ----------
per share Fair Market Value of the Common Stock at the time of such exercise;
minus (Y) the Exercise Price at the time of such exercise; divided by (ii) the
-----                                                      ----------
per share Fair Market Value of the Common Stock at the time of such exercise. An
exercise of a Warrant in accordance with the immediately preceding sentences is
herein called a "CASHLESS EXERCISE."

                  To the extent an exercise of a Warrant is not effected through
a Cashless Exercise, the Exercise Price shall be payable by certified check or
official bank check or by such other means as is acceptable to the Company in
the lawful currency of the United States of America which as of the time of
payment is legal tender for payment of public or private debts. The Company has
initially designated the principal corporate trust office of the Warrant Agent
in The City of Wilmington, Delaware, as the initial Warrant Agent Office. The
Exercise Price and the number and kind of Warrant Shares purchasable upon the
exercise of the Warrants is subject to adjustment upon the occurrence of certain
events set forth in the Warrant Agreement.

                  Any Warrants not exercised on or prior to 5:00 p.m., New York
City time, on April 12, 2006 shall expire and thereafter be void.

                  Reference is hereby made to the further provisions on the
reverse hereof which provisions shall for all purposes have the same effect as
though fully set forth at this place.

                                       2
<PAGE>

                  This Warrant Certificate shall not be valid unless
authenticated by the Warrant Agent, as such term is used in the Warrant
Agreement.

                  All terms used herein but not defined herein have the meanings
ascribed to such terms in the warrant agreement.

                  THIS WARRANT CERTIFICATE SHALL BE CONSTRUED IN ACCORDANCE WITH
THE LAWS OF THE STATE OF NEW YORK WITHOUT GIVING EFFECT TO THE CONFLICT OF LAWS
PROVISIONS THEREOF.

                  WITNESS the seal of the Company and signatures of its duly
authorized officers.

Dated:

                                            AIRTRAN HOLDINGS, INC.


                                            By: /s/ Steven A. Rossum
                                                --------------------------------
                                                     Steven A. Rossum
                                                     Vice President

                                            Certificate of Authentication:

                                            This is one of the Warrants referred
                                            to in the within mentioned Warrant
                                            Agreement:

                                            WILIMINGTON TRUST COMPANY,
                                            as Warrant Agent

                                            By: /s/ James P. Lawler
                                                --------------------------------
                                            Name:  James P. Lawler
                                            Title: Vice President

                                       3
<PAGE>

                            AIRTRAN HOLDINGS, INC.

                  The Warrants evidenced by this Warrant Certificate are part of
a duly authorized issue of Warrants expiring at 5:00 p.m., New York City time,
on April 12, 2006, each of which represents the right to purchase at any time on
or after the Exercisability Date (as defined in the Warrant Agreement) and on or
prior to such date 18.02885 shares of Common Stock of the Company, subject to
adjustment as set forth in the Warrant Agreement. The Warrants are issued
pursuant to a Warrant Agreement dated as of April 12, 2001 (the "WARRANT
AGREEMENT"), duly executed and delivered by the Company to Wilmington Trust
Company, as Warrant Agent (the "WARRANT AGENT"), which Warrant Agreement is
hereby incorporated by reference in and made a part of this instrument and is
hereby referred to for a description of the rights, limitation of rights,
obligations, duties and immunities thereunder of the Warrant Agent, the Company
and the Holders (the words "Holders" or "Holder" meaning the registered Holder
or registered Holders) of the Warrants.

                  Warrants may be exercised by (i) surrendering at any Warrant
Agent Office this Warrant Certificate with the form of Election to Exercise set
forth hereon duly completed and executed and (ii) to the extent such exercise is
not being effected through a Cashless Exercise, paying in full the Warrant
Exercise Price for each such Warrant exercised and any other amounts required to
be paid pursuant to the Warrant Agreement.

                  If all of the items referred to in the last sentence of the
preceding paragraph are received by the Warrant Agent at or prior to 2:00 p.m.,
New York City time, on a Business Day, the exercise of the Warrant to which such
items relate will be effective on such Business Day. If any items referred to in
the last sentence of the preceding paragraph are received after 2:00 p.m., New
York City time, on a Business Day, the exercise of the Warrants to which such
item relates will be deemed to be effective on the next succeeding Business Day.
Notwithstanding the foregoing, in the case of an exercise of Warrants on April
12, 2006, if all of the items referred to in the last sentence of the preceding
paragraph are received by the Warrant Agent at or prior to 5:00 p.m., New York
City time, on such Expiration Date, the exercise of the Warrants to which such
items relate will be effective on the Expiration Date.

                  As soon as practicable after the exercise of any Warrant or
Warrants, but in no event later than the third business day after the Exercise
Date, the Company shall issue or cause to be issued to or upon the written order
of the registered Holder of this Warrant Certificate, a certificate or
certificates evidencing the Warrant Shares to which such Holder is entitled, in
fully registered form, registered in such name or names as may be directed by
such Holder pursuant to the Election to Exercise, as set forth on the reverse of
this Warrant Certificate. Such certificate or certificates evidencing the
Warrant Shares shall be deemed to have been issued and any persons who are
designated to be named therein shall be deemed to have become the Holder of
record of such Warrant Shares as of the close of business on the Exercise Date.
After such exercise of any Warrant or Warrants, the Company shall also issue or
cause to be issued to or upon the written order of the registered Holder of such
Warrant Certificate, a new Warrant Certificate, countersigned by the Warrant
Agent pursuant to the Company's written instruction, evidencing the number of
Warrants, if any, remaining unexercised (unless such Warrants shall have
expired).

                  The Company shall not be required to issue fractional shares
of Common Stock on the exercise of Warrants. If more than one Warrant shall be
presented for exercise in full at the same time by the same Holder, the number
of full shares of Common Stock which shall be issuable upon such exercise shall
be computed on the basis of the aggregate number of shares of Common Stock which
may be acquired on exercise of the Warrants so presented. If any fraction of a
share of Common Stock would be issuable on the exercise of any Warrant or
Warrants, the Company shall either (i) pay an amount in cash calculated by the
Company to equal the per share Fair Market Value of the Common Stock multiplied
by

                                       4
<PAGE>

such fraction of a share of Common Stock computed to the nearest whole cent or
(ii) aggregate all such fractional shares of Common Stock into a whole number of
shares and sell such aggregated fractional shares on behalf of the Holders
entitled thereto in a public or private sale and distribute, on a pro rata
basis, the net cash proceeds therefrom to such Holders. While the Company will
use its best efforts to secure the best available sale price for such aggregated
fractional shares, such price shall not necessarily be the highest price
obtainable for such shares. By their acceptances of the Warrant Certificates,
Holders expressly waive any and all rights to receive any fraction of a share of
Common Stock or a stock certificate or scrip representing a fraction of a share
of Common Stock.

                  Warrant Certificates, when surrendered at any office or agency
maintained by the Company for that purpose by the registered Holder thereof in
person or by legal representative or attorney duly authorized in writing, may be
exchanged for a new Warrant Certificate or new Warrant Certificates evidencing
in the aggregate a like number of Warrants, in the manner and subject to the
limitations provided in the Warrant Agreement, without charge except for any tax
or other governmental charge imposed in connection therewith.

                  Upon due presentment for registration of transfer of this
Warrant Certificate at any office or agency maintained by the Company for that
purpose, a new Warrant Certificate evidencing in the aggregate a like number of
Warrants shall be issued to the transferee in exchange for this Warrant
Certificate, subject to the limitations provided in the Warrant Agreement,
without charge except for any tax or other governmental charge imposed in
connection therewith.

                  The Company and the Warrant Agent may deem and treat the
registered Holder hereof as the absolute owner of this Warrant Certificate
(notwithstanding any notation of ownership or other writing hereon made by
anyone) for the purpose of any exercise hereof and for all other purposes, and
neither the Company nor the Warrant Agent shall be affected by any notice to the
contrary.

                                       5
<PAGE>

                        (FORM OF ELECTION TO EXERCISE)

        (To be executed upon exercise of Warrants on the Exercise Date)


                  The undersigned hereby irrevocably elects to exercise [ ] of
the Warrants represented by this Warrant Certificate and purchase the whole
number of Warrant Shares issuable upon the exercise of such Warrants and
herewith tenders payment for such Warrant Shares in the amount of $[ ] in cash
or by certified or official bank check, in accordance with the terms hereof. In
lieu of payment of the cash exercise price, the Holder hereof is electing to
exercise [ ] Warrants pursuant to a Cashless Exercise for [ ] shares of Common
Stock. The undersigned requests that a certificate representing such Warrant
Shares be registered in the name of ______________________ whose address is
_____________________________ and that such certificate be delivered to
___________________________ whose address is __________________________. Any
cash payments to be paid in lieu of a fractional Warrant Share should be made to
__________________ whose address is ________________________ and the check
representing payment thereof should be delivered to ______________________ whose
address is ______________________.

Dated:                    Name of Holder of
                          Warrant Certificate:________________________________

                          ----------------------------------------------------
                          (Please Print)

                          Tax Identification or
                          Social Security Number:_____________________________


                          Address:____________________________________________

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

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


                          Signature: _________________________________________


                          Note: The above signature must correspond with the
                          name as written upon the face of this Warrant
                          Certificate in every particular, without alteration or
                          enlargement or any change whatever.

                                       6
<PAGE>

                          Dated: ----------------------------------------------

                          Signature: ------------------------------------------

                          Note: The above signature must correspond with the
                          name as written upon the face of this Warrant
                          Certificate in every particular, without alteration or
                          enlargement or any change whatever.

                          Signature Guaranteed: -------------------------------

                                       7