<PAGE>

                                                                    EXHIBIT 4.38


                      SECOND AMENDMENT dated as of January 11, 2001 (this
                      "Amendment"), to the Credit Agreement (the "Credit
                       ---------                                  ------
                      Agreement") dated as of May 31, 2000, as amended pursuant
                      ---------
                      to a First Amendment dated as of December 7, 2000, among
                      McLEODUSA INCORPORATED, a Delaware corporation (the
                      "Borrower"); the lenders party thereto (the "Lenders");
                       --------                                    -------
                      THE CHASE MANHATTAN BANK, a New York banking corporation,
                      as administrative agent (in such capacity, the
                      "Administrative Agent") and as collateral agent (in such
                       --------------------
                      capacity, the "Collateral Agent"); Salomon Smith Barney
                                     ----------------
                      Inc., as syndication agent (in such capacity, the
                      "Syndication Agent"); and Bank of America, N.A. and
                       -----------------
                      Goldman Sachs Credit Partners L.P., as co-documentation
                      agents (in such capacities, the "Co-Documentation
                                                       ----------------
                      Agents").
                      ------

           The Borrower has requested that the Lenders amend certain provisions
of the Credit Agreement, and the Lenders are willing so to amend the Credit
Agreement on the terms and subject to the conditions set forth herein.
Capitalized terms used herein and not otherwise defined herein shall have the
meanings assigned to such terms in the Credit Agreement.

           Accordingly, in consideration of the mutual agreements herein
contained and other good and valuable consideration, the sufficiency and receipt
of which are hereby acknowledged, the parties hereto agree as follows:

           SECTION 1.  Amendment of Credit Agreement.  The Credit Agreement is
                       -----------------------------
hereby amended, effective as of the Amendment Effective Date, as follows:

           (a)  Amendment of Section 1.01.
                -------------------------

                  (i) The following definitions are inserted in alphabetical
        order in Section 1.01 of the Credit Agreement:

                  ""Series B Preferred Stock" means the Series B Cumulative
                    ------------------------
        Convertible Preferred Stock, par value $0.01 per share, of the
        Borrower."

                  ""Series C Preferred Stock" means the Series C Cumulative
                    ------------------------
        Convertible Preferred Stock, par value $0.01 per share, of the
        Borrower."

                  (ii) The definition of "Change of Control" in Section 1.01 of
        the Credit Agreement is hereby amended by inserting the following
        proviso at the end of such definition:

                      "; provided that any event that constitutes a change of
                         --------
                      control under the Indentures or any future indenture
                      governing unsecured indebtedness issued by the Borrower
                      after the date hereof shall also constitute a "Change of
                      Control" under this Agreement."

           (b) Amendment of Section 6.01(b). Section 6.01(b) of the Credit
               ----------------------------
Agreement is hereby amended by (x) replacing the phrases "Series B Cumulative
Convertible Preferred Stock, par value
<PAGE>

$0.01 per share (the "Series B Preferred Stock")," and "Series C Cumulative
                      ------------------------
Convertible Preferred Stock, par value $0.01 per share, of the Borrower" with
the defined terms "Series B Preferred Stock" and "Series C Preferred Stock",
respectively.

           (c)  Amendment of Section 6.09(a).  Section 6.09(a) of the Credit
                ----------------------------
Agreement is hereby amended as follows:

                      (i)   the phrase "and (v)" is hereby replaced with the
           following phrase:

                          ", (v) following the repayment of all outstanding
                      Loans and Letters of Credit and the termination of all
                      outstanding Commitments hereunder, the Borrower may redeem
                      the Series B Preferred Stock and the Series C Preferred
                      Stock at any time after September 15, 2006 in accordance
                      with the terms thereof, (vi) the Borrower may redeem the
                      Series B Preferred Stock and the Series C Preferred Stock
                      within 180 days after September 15, 2009 if so requested
                      by the holders of such Series B Preferred Stock or Series
                      C Preferred Stock, as the case may be, in accordance with
                      the terms thereof provided that no Event of Default is
                      continuing or would result therefrom and (vii)"; and

                      (ii)   the phrase "this clause (v)" in the proviso thereto
           is replaced with the phrase "clause (vii) preceding".

           (d)  Amendment of Section 6.09(b).  Section 6.09(b) of the Credit
                ----------------------------
Agreement is hereby amended as follows:

                      (i)   the following parenthetical is hereby inserted
           immediately following the words "New Preferred Stock" at the end of
           clause (i) of such Section:

                                "(it being understood that this Section 6.09(b)
                            shall not be deemed to prohibit the existence of the
                            provisions contained in Section 4.08 of the
                            Indentures permitting certain holders of
                            Indebtedness of the Borrower to require the
                            repurchase of such Indebtedness following certain
                            sales of assets of the Borrower (other than the
                            Indenture specified in clause (b) of the definition
                            of "Indentures," in which such sale of assets is
                            specified in Section 4.09 thereof) or such
                            substantially similar provisions as may be contained
                            in future indentures governing unsecured
                            indebtedness issued by the Borrower after the
                            Effective Date; provided that no such repurchases
                                            --------
                            shall be effected so long as any Loans, Letters of
                            Credit or Commitments are outstanding under this
                            Agreement)";

                      (ii)  the word "and" at the end of clause (iii) of such
                            Section is hereby deleted; and

                      (iii) the following phrase is hereby inserted at the end
                            of clause (iv) of such Section: "; and (v) payments
                            to redeem outstanding Indebtedness pursuant to the
                            exercise of certain rights of the holders of such
                            Indebtedness to require the repurchase of such
                            Indebtedness arising in the event of a change in
                            control of the Borrower specified in Section 4.07 of
                            each of the Indentures or such substantially similar
                            provisions as may be contained in future indentures
<PAGE>

                            governing unsecured indebtedness issued by the
                            Borrower after the date hereof."

           (e) Amendment of Section 6.11. Section 6.11 of the Credit Agreement
               --------------------------
is hereby amended by replacing the phrase "or the Indentures" in clause (i) of
the proviso the reto with the following phrase:

           ", the Indentures or any provisions restricting or imposing
        conditions upon Liens as may be contained in future indentures governing
        unsecured indebtedness issued by the Borrower after the Effective Date
        provided that such provisions are no more restrictive than the
        provisions restricting or imposing conditions upon Liens contained in
        the Indentures on May 31, 2000."

           SECTION 2. Representations and Warranties. To induce the other
                      ------------------------------
parties hereto to enter into this Amendment, the Borrower represents and
warrants to each of the Lenders, the Administrative Agent and the Collateral
Agent that, as of the Amendment Effective Date:

           (a) The representations and warranties set forth in Article III of
the Credit Agreement are true and correct in all material respects on and as of
the Amendment Effective Date with the same effect as though made on and as of
the Amendment Effective Date, except to the extent such representations and
warranties expressly relate to an earlier date.

           (b) After giving effect to the agreements and waivers herein, no
Default or Event of Default has occurred and is continuing.

           SECTION 3. Effectiveness. This Amendment shall become effective on
                      -------------
the date (the "Amendment Effective Date") that the Administrative Agent shall
               ------------------------
have received counterparts of this Amendment that, when taken together, bear the
signatures of the Borrower and the Required Lenders. Once effective, this
Amendment shall be retroactive to May 31, 2000.

           SECTION 4. Effect of Amendment. Except as expressly set forth herein,
                      -------------------
this Amendment shall not by implication or otherwise limit, impair, constitute a
waiver of or otherwise affect the rights and remedies of the Lenders, the
Administrative Agent or the Collateral Agent under the Credit Agreement or any
other Loan Document, and shall not alter, modify, amend or in any way affect any
of the terms, conditions, obligations, covenants or agreements contained in the
Credit Agreement or any other provision of the Credit Agreement or any other
Loan Document, all of which are ratified and affirmed in all respects and shall
continue in full force and effect. Nothing herein shall be deemed to entitle the
Borrower to a consent to, or a waiver, amendment, modification or other change
of, any of the terms, conditions, obligations, covenants or agreements contained
in the Credit Agreement or any other Loan Document in similar or different
circumstances. This Amendment shall apply and be effective only with respect to
the provisions of the Credit Agreement specifically referred to herein.

           SECTION 5. Counterparts. This Amendment may be executed in any number
                      ------------
of counterparts and by different parties hereto in separate counterparts, each
of which when so executed and delivered shall be deemed an original, but all
such counterparts together shall constitute but one and the same instrument.
Delivery of any executed counterpart of a signature page of this Amendment by
facsimile transmission shall be as effective as delivery of a manually executed
counterpart hereof.
<PAGE>

           SECTION 6.  Applicable Law. THIS AMENDMENT SHALL BE GOVERNED BY, AND
                       --------------
CONSTRUED IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK.

           SECTION 7.  Headings. The headings of this Amendment are for purposes
                       --------
of reference only and shall not limit or otherwise affect the meaning hereof.
<PAGE>

           IN WITNESS WHEREOF, the parties hereto have caused this Amendment to
be duly executed by their duly authorized officers, all as of the date and year
first above written.

                                   McLEODUSA INCORPORATED

                                      by

                                   _________________________________
                                         Name:
                                         Title:


                                   Acknowledged and Agreed:

                                   EACH OF THE SUBSIDIARIES
                                   LISTED AS SUBSIDIARY GUARANTORS
                                   ON SCHEDULE I TO THE
                                   SUBSIDIARY GUARANTEE AGREEMENT,

                                      by
                                         ___________________________

                                         Name:
                                         Title:  Authorized Officer
<PAGE>

                                    THE CHASE MANHATTAN BANK,
                                    individually and as Agent

                                       by
                                    _________________________________
                                          Name:
                                          Title:
<PAGE>

                                   Name of Institution:

                                        by

                                    _________________________________
                                          Name:
                                          Title: