<PAGE>
 
                                                                     EXHIBIT 3.1
 
                            AMENDED AND RESTATED

                          ARTICLES OF INCORPORATION

                                     OF

                           TIER TECHNOLOGIES, INC.

     James L. Bildner and George K. Ross do hereby certify that:

     FIRST:    They are the duly elected and acting Chairman of the Board and
               Chief Executive Officer, and Executive Vice President and Chief
               Financial Officer, respectively, of TIER TECHNOLOGIES, INC., a
               California corporation (the "Corporation").

     SECOND:   The Articles of Incorporation of this corporation are amended and
               restated in full to read as follows:

                                  ARTICLE I

     The name of the Corporation is TIER TECHNOLOGIES, INC.

                                 ARTICLE II

     The purpose of the Corporation is to engage in any lawful act or activity
for which a corporation may be organized under the General Corporation Law of
California other than the banking business, the trust company business, or the
practice of a profession permitted to be incorporated by the California
Corporations Code.

                                 ARTICLE III

     A.  AUTHORIZED CAPITALIZATION.  The Corporation is authorized to issue
three classes of shares designated "Class A Common Stock," "Class B Common
Stock" and "Preferred Stock," respectively.  The total number of shares of all
classes of stock that the Corporation shall have authority to issue is forty-
eight million, eight hundred thirty-eight thousand, eight hundred nine
(48,838,809) shares.  The number of shares of Class A Common Stock that the
Corporation is authorized to issue is one million, six hundred fifty-nine
thousand, seven hundred sixty-two (1,659,762) shares.  The number of shares of
Class B Common Stock that the Corporation is authorized to issue is forty-two
million, six hundred thousand (42,600,000) shares.  The number of shares of
Preferred Stock that the Corporation is authorized to issue is four million,
five hundred seventy-nine thousand, forty-seven (4,579,047) shares.

     B.  PREFERRED STOCK.  The Preferred Stock may be issued from time to
time in one or more series.  Except as otherwise provided in this Article III,
the Board of Directors is hereby authorized to determine and alter the rights,
preferences, privileges and restrictions granted to or imposed upon any wholly
unissued series of Preferred Stock, and to fix the number of shares of any such
series of Preferred Stock, and the designation of any such series of Preferred
Stock.  The Board of Directors, within the limits and restrictions stated in
this Article 
<PAGE>
 
III or any resolution of the Board of Directors originally fixing the number
of shares constituting any series, may increase or decrease (but not below the
number of shares of such series then outstanding) the number of any series
subsequent to the issuance of shares of that series.

     C.  CLASS A COMMON STOCK.  The shares of Class A Common Stock and shares of
Class B Common Stock shall be identical in all respects and shall have equal
rights and privileges, except as set forth in this paragraph C and in paragraph
D of this Article III.  Upon dissolution of the Corporation, the Class A Common
Stock and Class B Common Stock are entitled to share ratably in the assets
thereof that may be available for distribution after satisfaction of creditors
and the payment of any liquidation preference of any outstanding shares of
Preferred Stock.

         1.  DIVIDENDS.

             (a) Subject to the provisions of Section C.1(b) below with
respect to dividends or distributions in shares of Class A Common Stock or
shares of Class B Common Stock: (i) such dividends or distributions as may be
determined from time to time may be declared and paid or made upon each share
of Class A Common Stock out of any source at the time lawfully available for
the payment of dividends, provided that concurrently identical dividends or
distributions are declared and paid or made upon each share of Class B Common
Stock and (ii) such dividends or distributions as may be determined from time
to time may be declared and paid or made upon each share of Class B Common
Stock out of any source at the time lawfully available for the payment of
dividends, provided that concurrently identical dividends or distributions are
declared and paid or made upon each share of Class A Common Stock.

             (b) No dividend may be declared or paid or made upon any share of
the Corporation in shares of Class A Common Stock. In the event that a
dividend or distribution is declared and paid or made upon shares of Class A
Common Stock in shares of Class B Common Stock, concurrently an identical
dividend or distribution must be declared and paid or made upon each share of
Class B Common Stock in shares of Class B Common Stock and in the event that a
dividend or distribution is declared and paid or made upon shares of Class B
Common Stock in shares of Class B Common Stock, concurrently an identical
dividend or distribution must be declared and paid or made upon each share of
Class A Common Stock in shares of Class B Common Stock.

         2.  STOCK COMBINATIONS AND SUBDIVISIONS.  The Corporation shall not
effect a combination (reverse stock split) or a subdivision (stock split) of
either the Class A Common Stock or the Class B Common Stock except in compliance
with the following: (i) the Class A Common Stock shall not be combined or
subdivided unless at the same time there is a proportionate combination or
subdivision of the Class B Common Stock, (ii) the Class B Common Stock shall not
be combined or subdivided unless at the same time there is a proportionate
combination or subdivision of the Class A Common Stock and (iii) neither the
Class A Common Stock nor the Class B Common Stock shall be combined or
subdivided unless an amendment to these Amended and Restated Articles of
Incorporation is approved by (in addition to any other approval by holders of
shares of the Corporation which may be required) 

                                      2
<PAGE>
 
the holders of shares of Class B Common Stock as provided in subsection D.3(c)
of this Article III.

          3.  VOTING.  Subject to the provisions of subsection D.3 of this
Article III and except as otherwise required by applicable law related to class
voting rights, the holders of Class A Common Stock shall vote together with the
holders of Class B Common Stock as a single class, provided that the holders of
Class A Common Stock shall have ten (10) votes per share and the holders of
Class B Common Stock shall have one (1) vote per share on all matters that may
be submitted to a vote or consent of the shareholders.  Without limiting the
generality of the foregoing:

              (a) With respect to the election of Directors (whether such
election is by vote at a meeting of shareholders or by written consent of
shareholders), the holders of Class A Common Stock and Class B Common Stock
shall be entitled, voting as a single class to elect the remaining Directors
not subject to the priority right of the holders of Class B Common Stock to
elect one or more Directors as set forth in Subsection D.3(a) of this Article
III. Vacancies on the Board of Directors created by (i) the death, resignation
or removal of a Director who was elected by the holders of Class A Common
Stock and Class B Common Stock voting as a single class or (ii) an increase in
the authorized number of Directors if such vacancy is not to be filled by the
holders of Class B Common Stock voting as a separate class in accordance with
Section D.3(a) of this Article III, may be filled by those Directors (acting
by majority vote, though less than a quorum, or by the act of a sole remaining
Director) who were elected by the holders of Class A Common Stock and Class B
Common Stock voting as a single class.

              (b) Except as may otherwise be required by law, any Director
elected by the holders of Class A Common Stock and Class B Common Stock voting
as a single class, or who was elected by those Directors who were elected by
the holders of Class A Common Stock and Class B Common Stock voting as a
single class to fill a vacancy, may be removed from office with or without
cause by the holders of shares of Class A Common Stock and Class B Common
Stock voting as a single class, provided that, to the extent permitted by
applicable law, any such Director may be removed for cause by the Board of
Directors.

          4.  CONVERSION.

              (a) Each share of Class A Common Stock shall be convertible, at
the option of the holder thereof, at any time after the date of issuance of
such share, at the office of the Corporation or any transfer agent for the
Class A Common Stock, into one fully paid and non-assessable share of Class B
Common Stock.

              (b) Each share of Class A Common Stock shall automatically be
converted into one share of Class B Common Stock in the event that the record or
beneficial ownership of such share of Class A Common Stock shall be transferred
in any manner or for any reason, voluntarily or involuntarily, by operation of
law or otherwise, provided, however, that if the beneficial or record ownership
                  ------------------                                           
of such share of Class A Common Stock is transferred (i) by any holder of Class
A Common Stock to a voting trust created for the holders of Class A Common Stock
("Voting Trust"), (ii) from such Voting Trust to the holder that transferred
such share of Class A Common Stock into the Voting Trust, or (iii) to any person
who was the beneficial holder of fifteen percent (15%) or more of the issued and
outstanding shares of Class 

                                      3
<PAGE>
 
A Common Stock (and who was also either the record holder of such shares of
Class A Common Stock or the record holder of one or more voting trust
certificates ("Voting Trust Certificates") for such shares of Class A Common
Stock held in the Voting Trust) as of the date of filing of these Amended and
Restated Articles of Incorporation with the California Secretary of State (the
"Filing Date"), regardless of the number of such shares of Class A Common Stock,
if any, held by such person on any subsequent date (each such person being
referred to as a "15% Class A Holder"), (including, for purposes of this clause
(iii), transfers to 15% Class A Holders which occur by means of a transfer of
record or beneficial ownership of one or more Voting Trust Certificates), then
such share of Class A Common Stock which is transferred as described in clause
(i), (ii) or (iii) shall not be converted into a share of Class B Common Stock,
and provided, further, that any share of Class A Common Stock which is
                      ----------------------                                 
transferred as described in clause (i), (ii) or (iii) shall remain subject to
the provisions of this Section C.4 of Article III. A pledge of Class A Common
Stock as security for an obligation of a holder of such stock shall not be
considered a transfer for purposes of this paragraph, unless and until
beneficial ownership is transferred to the pledgeholder. The conversion into
Class B Common Stock shall be deemed to have occurred (whether or not
certificates representing such shares are surrendered) as of the close of
business on the date of transfer, and the person or persons entitled to receive
shares of Class B Common Stock issuable upon such conversion shall be treated
for all purposes as the record holder or holders of such shares of Class B
Common Stock on that date. For purposes of this Section C.4 of Article III,
"beneficial ownership" shall be determined in accordance with Rule 13d-3
promulgated under the Securities Exchange Act of 1934, as amended, as in effect
on the Filing Date.

          (c) Before any shares of Class B Common Stock shall be delivered upon
conversion, the holder of shares of Class A Common Stock whose shares have been
converted into Class B Common Stock shall deliver the certificate(s)
representing such shares to the Corporation or its duly authorized agent (or if
such certificates have been lost, stolen or destroyed, such holder shall execute
an agreement satisfactory to the Corporation to indemnify the Corporation from
any loss incurred by it in connection with such conversion), specifying the
place where the Common Stock issued in conversion thereof shall be sent.  The
endorsement of the certificates shall be in a form satisfactory to the
Corporation or such agent, as the case may be.

          (d) The Corporation shall, at all times, reserve and keep available
out of the authorized and unissued shares of Class B Common Stock, solely for
the purpose of effecting the conversion of the outstanding Class A Common Stock,
such number of shares of Class B Common Stock as shall from time to time be
sufficient to effect the conversion of all of the outstanding Class A Common
Stock and if, at any time, the number of authorized and unissued shares of Class
B Common Stock shall not be sufficient to effect conversion of the then
outstanding Class A Common Stock, the Corporation shall take such corporate
action as may be necessary to increase the number of authorized and unissued
shares of Class B Common Stock to such number as shall be sufficient for such
purposes.

          (e) The Corporation shall pay any and all issuance and other taxes
that may be payable in respect of any issuance or delivery of shares of Class B
Common Stock on conversion of Class A Common Stock.  The Corporation shall not,
however, be required to pay any tax which may be payable with respect to the
issuance of any Class B Common Stock in a 

                                       4
<PAGE>
 
name other than that in which the Class A Common Stock so converted was
registered, and no such issuance or delivery shall be made unless and until
the person requesting such issuance has paid to the Corporation the amount of
any such tax, or has established, to the satisfaction of the Corporation, that
such tax has been paid.

             (f) All shares of Class B Common Stock which may be issued upon
conversion of the shares of Class A Common Stock will, upon issuance by the
Corporation, be validly issued, fully paid and non-assessable and free from all
taxes, liens and charges with respect to the issuance thereof.

             (g) All certificates representing shares of Class A Common Stock
surrendered for conversion or otherwise acquired by the Corporation (all such
shares being referred to as "Converted Shares") shall be appropriately canceled
on the books of the Corporation.  Such shares shall not be reissuable by the
Corporation and the authorized number of shares of Class A Common Stock of the
Corporation shall be reduced by such amount.  Within ninety (90) days after each
anniversary of the Filing Date referred to in subsection C.4(b) of this Article
III the Corporation shall file with the California Secretary of State an
amendment (a "Reduction Amendment") to these Amended and Restated Articles of
Incorporation to reflect the reduction in the authorized number of shares of
Class A Common Stock by an amount equal to the number of Converted Shares which
have become Converted Shares since the most recent to occur of the Filing Date
or the date of filing of the immediately prior Reduction Amendment or other
amendment to these Amended and Restated Articles of Incorporation ("Other
Amendment") (such shares being referred to as "New Converted Shares"), provided
                                                                       --------
that, (i) the Corporation shall not be required to file a Reduction Amendment
-----                                                                        
unless the number of New Converted Shares shall equal at least 50,000 (adjusted
for any stock dividends, combinations or subdivisions subsequent to the Filing
Date), (ii) if on any occasion the Corporation shall elect to file an Other
Amendment, then it shall include in such Other Amendment provisions to reflect
any reduction in the authorized number of shares of Class A Common Stock due to
such shares having become New Converted Shares since the most recent to occur of
the Filing Date or the date of filing of the immediately prior Reduction
Amendment or Other Amendment, and (iii) if one or more Reduction Amendments
cannot be filed with the California Secretary of State without obtaining
approval of some or all of the shareholders of the Corporation, the Corporation
shall not be required to file such Reduction Amendments, and in that case it
shall follow the procedure indicated in clause (ii) above, and when all of the
authorized shares of Class A Common Stock have been converted or otherwise
reacquired by the Corporation the Class A Common Stock shall be automatically
eliminated and these Amended and Restated Articles of Incorporation shall be
amended to eliminate any statement of rights, preferences, privileges and
restrictions relating solely to the Class A Common Stock.

     D.  CLASS B COMMON STOCK.

         1.  DIVIDENDS AND DISTRIBUTIONS.  Subject to the provisions of Section
C.1 of this Article III, dividends and distributions may be declared and paid or
made upon the Class B Common Stock as may be permitted by applicable law.

                                      5
<PAGE>
 
          2.  STOCK COMBINATIONS AND SUBDIVISIONS.  Subject to the provisions of
paragraph C.2 of this Article III, the Class B Common Stock may be combined or
subdivided in such manner as may be permitted by applicable law.

          3.  VOTING.  The holders of the Class B Common Stock shall have the
voting rights set forth below in addition to the rights set forth in Section C.3
of this Article III:

              (a) With respect to the election of the Board of Directors
(whether such election is by vote at a meeting of shareholders or by written
consent of shareholders), the holders of Class B Common Stock, voting as a
separate class, shall be entitled to elect that number of Directors which is
the largest integral number which is less than fifty percent (50%) of the
authorized number of Directors. Such election shall be from a slate of
Director nominees separate from a slate of Director nominees from which
holders of Class A Common Stock and Class B Common Stock voting as a single
class shall elect Directors. Vacancies on the Board of Directors created by
(i) the death, resignation or removal of a Director who was elected by the
holders of Class B Common Stock or (ii) by an increase in the authorized
number of Directors, if such vacancy is to be filled by the holders of Class B
Common Stock voting as a separate class in accordance with the immediately
preceding sentence, may be filled by those Directors (acting by majority vote,
though less than a quorum, or by the act of a sole remaining Director) who
were elected by the holders of Class B Common Stock.

              (b) The holders of Class B Common Stock will be entitled to vote
as a separate class on the removal, with or without cause, of any Director
elected by the holders of Class B Common Stock; provided that, to the extent
permitted by applicable law, any such Director may be removed for cause by the
Board of Directors.

              (c) The Corporation shall not, without the vote or written
consent of the holders of a majority of the then outstanding shares of Class B
Common Stock, voting together as a single class:

                  (i)   increase the total number of authorized shares of
Class A Common Stock; or

                  (ii)  amend these Amended and Restated Articles of
Incorporation or the Corporation's Bylaws if such amendment would change any
of the rights, preferences or privileges provided for the benefit of the Class
B Common Stock or would increase the rights, preferences or privileges of the
Class A Common Stock.

              (d) At any meeting of the Corporation's shareholders at which
directors are elected or at which a vote is taken on the removal of a director
or directors elected by the holders of Class B Common Stock pursuant to
subsection D.3(a) of this Article III, then, in addition to any other quorum
requirement which must be satisfied, the presence, either in person or by proxy,
of the holders of a majority of the then outstanding shares of Class B Common
Stock shall be required to constitute a quorum for such meeting.

     E.  VOTING RIGHTS IF ONLY ONE CLASS OUTSTANDING.  Notwithstanding anything
in these Amended and Restated Articles of Incorporation to the contrary, the
holders of Class B Common Stock shall have exclusive voting power on all matters
at any time when no shares of 

                                      6
<PAGE>
 
Class A Common Stock or Preferred Stock are issued and outstanding and the
holders of Class A Common Stock shall have exclusive voting power on all
matters at any time when no shares of Class B Common Stock or Preferred Stock
are issued and outstanding.

                                 ARTICLE IV

     A.  LIABILITY FOR MONETARY DAMAGES.  The liability of the directors of the
Corporation for monetary damages shall be eliminated to the fullest extent
permissible under California law.

     B.  INDEMNIFICATION.  This Corporation is authorized to provide
indemnification of agents (as defined in Section 317 of the California
Corporations Code) for breach of duty to the Corporation and its shareholders
through bylaw provisions or through agreements with the agents, or through
shareholder resolutions, or otherwise, in excess of the indemnification
otherwise permitted by Section 317 of the Corporations Code, subject to the
limits on such excess indemnification set for in Section 204 of the Corporations
Code.

                                  ARTICLE V

     Effective on the first date when the Corporation has outstanding securities
designated as qualified for trading as a national market system security on the
National Association of Securities Dealers Automated Quotation System (or any
successor national market system) and has at least 800 holders of its equity
securities as of the record date for the Corporation's most recent annual
meeting of shareholders, the ability of shareholders to cumulate votes in the
election of directors shall be automatically eliminated.

     THIRD:  The foregoing Amended and Restated Articles of Incorporation have
been duly approved by the Board of Directors.

     FOURTH:  The foregoing Amended and Restated Articles of Incorporation may
be adopted with approval by the Board of Directors alone on the basis of
Sections 510(b)(1), 510(b)(2) and 510(f) of the Corporations Code because (i)
all of the authorized shares of the Corporation's Series A Convertible Preferred
Stock have been reacquired by the Corporation and the Articles of Incorporation
are being amended to reduce the authorized number of shares of Preferred Stock,
the class to which the Series A Convertible Preferred Stock belonged, by the
number of shares so reacquired and to eliminate any statement of rights,
preferences, privileges and restrictions relating solely to that series, and
(ii) less than all of the authorized, issued and outstanding shares of the
Corporation's Class A Common Stock have been reacquired by the Corporation, and,
as required by Article III, paragraph 4(g) of the Corporation's Articles of
Incorporation, the Articles of Incorporation are being amended to reduce the
authorized number of shares of Class A Common Stock by the number of shares so
reacquired.

                                      7
<PAGE>
 
     James L. Bildner and George K. Ross further declare under penalty of
perjury under the laws of the State of California that the matters set forth in
this certificate are true and correct of their own knowledge.

Dated:  July 15, 1998, at Walnut Creek, California
        -------------
 

/s/ James L. Bildner
-----------------------------
James L. Bildner
Chairman of the Board and
Chief Executive Officer

 

/s/ George K. Ross
-----------------------------
George K. Ross
Executive Vice President and
Chief Financial Officer

                                      8