<PAGE>

                                                                    EXHIBIT 4.12

                         SUBSIDIARY GUARANTY AGREEMENT
                           (FIBERNET TELECOM, INC.)

     This GUARANTY (as amended, supplemented, amended and restated or otherwise
modified from time to time, this "Guaranty"), entered into as of April 11, 2000
by FIBERNET TELECOM, INC., a Delaware corporation (the "Guarantor"), in favor of
DEUTSCHE BANK AG NEW YORK BRANCH, as administrative agent (together with any
successor(s) thereto in such capacity, the "Administrative Agent") for each of
the Secured Parties.

                                    RECITALS
                                    --------

     A.  Pursuant to the Credit Agreement, dated as of April 11, 2000 (as
amended, supplemented, amended and restated or otherwise modified from time to
time, the "Credit Agreement"), among Fibernet Telecom Group, Inc., a Delaware
corporation (the "Borrower"), the financial institutions from time to time
parties thereto (collectively, the "Lenders"), Deutsche Bank Securities Inc., as
co-syndications agent, Toronto Dominion (Texas), Inc., as co-syndications agent,
and the Administrative Agent, the Lenders have extended Commitments to make
Loans and issue Letters of Credit to, and for the benefit of, the Borrower;

     B.  The Guarantor has duly authorized the execution, delivery and
performance of this Guaranty;

     C.  It is in the best interests of the Guarantor to execute this Guaranty
as the Guarantor will derive substantial direct and indirect benefits from the
Loans made to the Borrower, and the Letters of Credit issued for the benefit of
the Borrower, from time to time pursuant to the Credit Agreement, including
receiving proceeds thereof which will enable the Guarantor to acquire
Telecommunication Assets comprising a portion of the System; and

     D.  This Guaranty is secured by the Subsidiary Security Agreement (FiberNet
Telecom, Inc.), dated as of the date hereof, between the Guarantor and the
Administrative Agent, as security for the Obligations.


                                   AGREEMENT
                                   ---------


     NOW, THEREFORE, in consideration of the premises and the mutual agreements
herein contained and for other good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, the parties hereto, intending to
be legally bound, agree as follows:
<PAGE>

                                  ARTICLE I.
                                 DEFINITIONS

Section 1.1  Defined Terms.
             --------------
     The following terms when used in this Guaranty shall have the following
meanings:

     "Administrative Agent" shall have the meaning assigned to such term in the
preamble.
--------

     "Borrower" shall have the meaning assigned to such term in the first
                                                                    -----
recital.
-------

     "Credit Agreement" shall have the meaning assigned to such term in the
first recital.
-------------

     "Guarantor" shall have the meaning assigned to such term in the preamble.
                                                                     --------

     "Guaranty" shall have the meaning assigned to such term in the preamble.
                                                                    --------

     "Lenders" shall have the meaning assigned to such term in the first
                                                                   -----
recital.
-------

     Section 1.2  Credit Agreement Definitions; Principles of Interpretation.
                  -----------------------------------------------------------

     Unless otherwise defined herein or the context otherwise requires, terms
used in this Guaranty, including its preamble and recitals, have the meanings
provided in the Credit Agreement (including the principles of interpretation set
forth in Section 1.3 of the Credit Agreement). All references herein to any
         -----------
rights or interests granted hereby to the Administrative Agent shall be deemed
to be rights or interests granted to the Administrative Agent for the benefit of
each of the Secured Parties, whether or not specifically so stated.

                                  ARTICLE II.
                              GUARANTY PROVISIONS

     Section 2.1  Guaranty.
                  ---------

     The Guarantor hereby, absolutely, unconditionally and irrevocably,
guarantees the full and punctual payment when due, whether at stated maturity,
by required prepayment, declaration, acceleration, demand or otherwise, of all
Obligations, provided, however, that the Guarantor shall be liable under this
             --------- -------
Guaranty only for the maximum amount of such liability that can be hereby
incurred without rendering this Guaranty voidable under applicable law relating
to fraudulent conveyance or fraudulent transfer (or similar concepts under
foreign law), and not for any greater amount.  This Guaranty constitutes a
guaranty of payment when due and not merely of collection, and the Guarantor
specifically agrees that it shall not be necessary or required that any Secured
Party or any holder of any Note exercise any right, assert any claim or demand
or enforce any remedy whatsoever against the Borrower or any other Loan Party
(or any other Person) before or as a condition to the performance of the
obligations of the Guarantor hereunder.

Section 2.2  Acceleration of Guaranty.
             -------------------------

                                       2
<PAGE>

     If an Event of Default of the nature set forth in Section 7.4 or 7.5 of the
                                                       -----------    ---
Credit Agreement with respect to the Borrower or any of its Subsidiaries shall
occur and be continuing, all of the Obligations shall, as set forth in Article
                                                                       -------
VII of the Credit Agreement, be immediately due and payable, and, accordingly,
---
the Guarantor shall be required to pay to the Administrative Agent, for the
benefit of the Secured Parties, forthwith an amount equal to all of the
Obligations.

     Section 2.3  Guaranty Absolute, Etc.
                  -----------------------

     This Guaranty shall in all respects be a continuing, absolute,
unconditional and irrevocable guaranty of payment, and shall remain in full
force and effect until all Obligations have been paid in full in cash, all
obligations of the Guarantor hereunder have been paid in full in cash, all
Interest Rate Agreements to which any Secured Party is a party have been
terminated and all Commitments have been terminated.  The Guarantor guarantees
that the Obligations will be paid strictly in accordance with the terms of the
Credit Agreement and each other Loan Document under which they arise.  The
liability of the Guarantor under this Guaranty shall be absolute, unconditional
and irrevocable, irrespective of:

          (a) any lack of validity, legality or enforceability of the Credit
     Agreement, any Note, or any other Loan Document or any Interest Rate
     Agreement;

          (b) the failure of any Secured Party or any holder of any Note

              (i)  to assert any claim or demand or to enforce any right or
          remedy against the Borrower, any other Loan Party or any other Person
          (including any other guarantor) under the provisions of the Credit
          Agreement, any Note, any other Loan Document, any Interest Rate
          Agreement or otherwise, or

              (ii) to exercise any right or remedy against any other guarantor
          of, or collateral securing, any of the Obligations;

          (c) any change in the time, manner or place of payment of, or in any
     other term of, all or any of the Obligations, or any other extension or
     renewal of any Obligation of the Borrower or any other Loan Party;

          (d) any reduction, limitation, impairment or termination of any of the
     Obligations for any reason other than the written agreement of the Secured
     Parties to terminate the Obligations in full, including any claim of
     waiver, release, surrender, alteration or compromise, and shall not be
     subject to, and the Guarantor hereby waives any right to or claim of, any
     defense or setoff, counterclaim, recoupment or termination whatsoever by
     reason of the invalidity, illegality, nongenuineness, irregularity,
     compromise, unenforceability of, or any other event or occurrence
     affecting, any Obligations of the Borrower, any other Loan Party or
     otherwise;

                                       3
<PAGE>

          (e) any amendment to, rescission, waiver, or other modification of, or
     any consent to departure from, any of the terms of the Credit Agreement,
     any Note, any other Loan Document or any Interest Rate Agreement;

          (f) any addition, exchange, release, surrender or non-perfection of
     any collateral, or any amendment to or waiver or release or addition of, or
     consent to departure from, any other guaranty held by any Secured Party or
     any holder of any Note securing any of the Obligations; or

          (g) any other circumstance which might otherwise constitute a defense
     available to, or a legal or equitable discharge of, the Borrower, any other
     Loan Party, any surety or any guarantor.

     Section 2.4  Reinstatement, Etc.
                  -------------------

     The Guarantor agrees that this Guaranty shall continue to be effective or
be reinstated, as the case may be, if at any time any payment (in whole or in
part) of any of the Obligations is rescinded or must otherwise be restored by
any Secured Party or any holder of any Note upon the insolvency, bankruptcy or
reorganization of the Borrower, any other Loan Party or otherwise, all as though
such payment had not been made.

     Section 2.5  Waiver, Indemnification, Etc.
                  -----------------------------

     The Guarantor hereby waives promptness, diligence, notice of acceptance and
any other notice with respect to any of the Obligations and this Guaranty and
any requirement that the Administrative Agent, any other Secured Party or any
holder of any Note protect, secure, perfect or insure any security interest or
Lien, or any property subject thereto, or exhaust any right or take any action
against the Borrower, any other Loan Party or any other Person (including any
other guarantor) or entity or any collateral securing the Obligations, as the
case may be.  The Guarantor hereby agrees to indemnify and hold harmless the
Administrative Agent and each other Secured Party for any and all costs and
expenses (including reasonable attorney's fees and expenses) incurred in
enforcing any right under this Guaranty.

     Section 2.6  Subordination.
                  --------------

     Except as otherwise specifically provided in, or permitted by, this
Guaranty or the Credit Agreement, all existing and future indebtedness of, or
other obligations owed by, the Borrower to the Guarantor is hereby subordinated
to all obligations and liabilities hereby guaranteed. Without the prior written
consent of the Administrative Agent, such subordinated indebtedness shall not be
paid or withdrawn in whole or in part, nor shall the Guarantor accept any
payment of or on account of any such indebtedness, after the occurrence and
during the continuance of an Event of Default under the Credit Agreement.  Any
payment by the Borrower in violation of this Guaranty shall be received by the
Guarantor in trust for the Administrative Agent, and the Guarantor shall cause
the same to be paid to the Administrative Agent immediately upon demand by the
Administrative Agent on account of the Borrower's obligations and liabilities
hereby

                                       4
<PAGE>

guaranteed.  The Guarantor shall not assign all or any portion of such
indebtedness while this Guaranty remains in effect except upon prior written
notice to the Administrative Agent by which the assignee of any such
indebtedness agrees that the assignment is made subject to the terms of this
Guaranty, and that any attempted assignment of such indebtedness in violation of
the provisions hereof shall be void.

     Section 2.7  Postponement of Subrogation.
                  ----------------------------

     The Guarantor agrees that it will not exercise any rights which it may
acquire by way of rights of subrogation under this Guaranty, by any payment made
hereunder or otherwise, until the prior payment in full in cash of all of the
Obligations, the termination of all Interest Rate Agreements to which any
Secured Party is a party and the termination of all Commitments.  Any amount
paid to the Guarantor on account of any such subrogation rights prior to the
payment in full in cash of all of the Obligations shall be held in trust for the
benefit of the Secured Parties and each holder of a Note and shall immediately
be paid to the Administrative Agent for the benefit of the Secured Parties and
each holder of a Note and credited and applied against the Obligations of the
Borrower and each other Loan Party, whether matured or unmatured, such order as
the Administrative Agent shall elect; provided,  however, that if
                                      --------   -------

          (a) the Guarantor has made payment to the Secured Parties and each
     holder of a Note of all or any part of the Obligations, and

          (b) all Obligations have been paid in full in cash, all Interest Rate
     Agreements to which any Secured Party is a party have been terminated and
     all Commitments have been permanently terminated,

then, at the Guarantor's request, the Administrative Agent, on behalf of the
Secured Parties and the holders of the Notes, will execute and deliver to the
Guarantor appropriate documents (without recourse and without representation or
warranty) necessary to evidence the transfer by subrogation to the Guarantor of
an interest in the Obligations resulting from such payment by the Guarantor.  In
furtherance of the foregoing, for so long as any Obligations or Commitments
remain outstanding, the Guarantor shall refrain from taking any action or
commencing any proceeding against the Borrower or any other Loan Party (or any
of its or their successors or assigns, whether in connection with a bankruptcy
proceeding or otherwise) to recover any amounts in respect of payments made
under this Guaranty to any Secured Party or any holder of a Note, except that
the Guarantor may file a proof of claim in a bankruptcy proceeding with respect
to the Borrower or any other Loan Party in connection with any obligations owed
by such Loan Party to the Guarantor in the event that the Administrative Agent
has failed to file a proof of claim on the Guarantor's behalf by the second
business day before the due date for such filing.

     Section 2.8  Successors, Transferees and Assigns; Transfers of Notes, Etc.
                  -------------------------------------------------------------

     This Guaranty shall:

                                       5
<PAGE>

          (a) be binding upon the Guarantor, and the Guarantor's successors,
     transferees and assigns; and

          (b) be enforceable by the Administrative Agent and its successors and
     assigns, for the benefit of the Secured Parties.

Without limiting the generality of the foregoing clause (b), any Lender may
                                                 ----------
assign or otherwise transfer (in whole or in part) any Loan, Note or Commitment
held by it to any other Person or entity as permitted by, and in accordance with
the terms of, the Credit Agreement, and such other Person or entity shall
thereupon become vested with all rights and benefits in respect thereof granted
to such Lender under any Loan Document (including this Guaranty) or otherwise,
subject, however, to any contrary provisions in such assignment or transfer, and
to the provisions of Sections 9.1 and 9.16 of the Credit Agreement.
                     ------------     ----

     Section 2.9  Payments Free and Clear of Taxes, Etc.
                  --------------------------------------

          (a) All payments made by the Guarantor hereunder shall be made in
     accordance with Section 2.7 of the Credit Agreement as if such Section were
                     -----------
     incorporated herein substituting "Guarantor" in the place of "Borrower" in
     each place it appears in that Section.

          (b) Without prejudice to the survival of any other agreement of the
     Guarantor hereunder, the agreements and obligations of the Guarantor
     contained in this Section shall survive the payment in full in cash of the
     principal of and interest on the Loans and all other Obligations.

                                 ARTICLE III.
                        REPRESENTATIONS AND WARRANTIES

     The Guarantor hereby represents and warrants to each Secured Party that the
representations and warranties contained in Article IV of the Credit Agreement,
                                            ----------
insofar as such representations and warranties are applicable to the Guarantor
and its properties, are true and correct in all material respects, each such
representation and warranty set forth in such Article (insofar as applicable as
aforesaid) and all other terms of the Credit Agreement to which reference is
made therein, together with all related definitions and ancillary provisions,
being hereby incorporated into this Guaranty by reference as though specifically
set forth in this Article.

                                  ARTICLE IV.
                                COVENANTS, ETC.

     The Guarantor covenants and agrees that, so long as any portion of the
Obligations shall remain unpaid, any Interest Rate Agreements to which any
Secured Party is a party shall remain in full force and effect or any Lender
shall have any outstanding Commitment, the Guarantor shall, unless the Majority
Lenders shall otherwise consent in writing,

                                       6
<PAGE>

          (a) perform, comply with and be bound by all of the agreements,
     covenants and obligations contained in Article V of the Credit Agreement
                                            ---------
     which are applicable to the Guarantor or its properties, each such
     agreement, covenant and obligation contained in such Article and all other
     terms of the Credit Agreement to which reference is made therein, together
     with all related definitions and ancillary provisions, being hereby
     incorporated into this Guaranty by reference as though specifically set
     forth in this Article, and

          (b) perform, comply with and be bound by all of the agreements,
     covenants and obligations contained in Article VI of the Credit Agreement
                                            ----------
     which are applicable to the Guarantor or its properties, each such
     agreement, covenant and obligation contained in such Article and all other
     terms of the Credit Agreement to which reference is made therein, together
     with all related definitions and ancillary provisions, being hereby
     incorporated into this Guaranty by reference as though specifically set
     forth in this Article.

                                  ARTICLE V.
                           MISCELLANEOUS PROVISIONS

     Section 5.1  Binding on Successors, Transferees and Assigns; Assignment.
                  -----------------------------------------------------------

     In addition to, and not in limitation of, Section 2.8, this Guaranty shall
                                               -----------
be binding upon the Guarantor and its successors, transferees and assigns and
shall inure to the benefit of and be enforceable by the Administrative Agent and
its successors, transferees and assigns for the benefit of the Secured Parties
(to the full extent provided pursuant to Section 2.8); provided, however, that
                                         -----------   --------  -------
the Guarantor may not assign any of its obligations or rights hereunder without
the prior written consent of the Majority Lenders.

     Section 5.2  Delay and Waiver.
                  -----------------

     No failure or delay by the Administrative Agent in exercising any right or
power hereunder shall operate as a waiver thereof, nor shall any single or
partial exercise of any such right or power, or any abandonment or
discontinuance of steps to enforce such a right or power, preclude any other or
further exercise thereof or the exercise of any other right or power.

     Section 5.3  Setoff.
                  -------

     In addition to, and not in limitation of, any rights of any Secured Party
or any holder of a Note under applicable law, each Secured Party and each such
holder shall, upon the occurrence of any Event of Default, have the right to
appropriate and apply amounts to the payment of the obligations of the Guarantor
owing to it hereunder, whether or not then due; provided, however, that any such
                                                --------  -------
appropriation and application shall be subject to the provisions of Section 9.5
                                                                    -----------
of the Credit Agreement.

     Section 5.4  Pari Passu Obligation.
                  ----------------------

                                       7
<PAGE>

     The obligations of the Guarantor hereunder shall be at least pari passu
with its obligations in connection with any other senior indebtedness or
obligation incurred by the Guarantor.

     Section 5.5  Notices.
                  --------

     Except in the case of notices and other communications expressly permitted
to be given by telephone, all notices and other communications provided for
herein shall be in writing and shall be delivered by hand or overnight courier
service, mailed by certified or registered mail or sent by telecopy, as follows:

The Guarantor:                     FiberNet Telecom, Inc.
                                   570 Lexington Avenue
                                   3rd Floor
                                   New York, New York  10022
                                   Attn.: President
                                   Telecopy: (212) 421-8920

The Administrative Agent:          Deutsche Bank AG New York Branch
                                   31 West 52nd Street,
                                   New York, New York 10019
                                   Attention: Jon D. Storck
                                   Telecopy No.: (212) 469-3713

Any party hereto may change its address or telecopy number for notices and other
communications hereunder by notice to the other parties hereto.  All notices and
other communications given (a) to the Guarantor in accordance with the terms of
this Guaranty shall be deemed to have been given when sent (answerback received)
in the case of telecopy, when delivered, in the case of hand or overnight
courier service, and 5 days after mailing, in the case of certified or
registered mail, or (b) to any party hereto in accordance with the terms of this
Guaranty other than for purposes of the immediately preceding clause (a), shall
be deemed to have been given on the date of receipt.

     Section 5.6  Amendments and Waivers.
                  -----------------------

     No amendment, modification, termination or waiver of any provision of this
Guaranty or consent to any departure by the Guarantor therefrom shall be
effective unless the same shall be in writing and signed by the Administrative
Agent and the Guarantor and shall comply with the provisions set forth in
Section 9.6 of the Credit Agreement.  Each amendment, modification, termination
-----------
or waiver shall be effective only in the specific instance and for the specific
purpose for which it was given.

     Section 5.7  Headings.
                  ---------

     Section and subsection headings contained in this Guaranty are inserted for
convenience of reference only, shall not be deemed to be a part of this Guaranty
for any purpose, and shall

                                       8
<PAGE>

not in any way define or affect the meaning, construction or scope of any of the
provisions hereof.

     Section 5.8  Applicable Law; Entire Agreement.
                  ---------------------------------

     This Guaranty shall be governed by, and shall be construed and enforced in
accordance with, the internal laws of the State of New York, without regard to
conflicts of laws principles (other than Sections 5-1401 and 5-1402 of the
General Obligations Law of the State of New York).  This Guaranty and the other
Loan Documents constitute the entire understanding among the parties hereto with
respect to the subject matter hereof and supersede any prior agreements, written
or oral, with respect thereto.

     Section 5.9  Severability.
                  -------------

     The invalidity, illegality or unenforceability in any jurisdiction of any
provision in or obligation under this Guaranty shall not affect or impair the
validity, legality or enforceability of the remaining provisions or obligations
under this Guaranty or of such provision or obligation in any other
jurisdiction.

     Section 5.10  Consent to Jurisdiction.
                   ------------------------

     The Guarantor hereby irrevocably and unconditionally submits, for itself
and its property, to the nonexclusive jurisdiction of the Supreme Court of the
State of New York sitting in New York County and of the United States District
Court of the Southern District of New York, and any appellate court in respect
thereof, in any action or proceeding arising out of or relating to this
Guaranty, or for recognition or enforcement of any judgment, and hereby
irrevocably and unconditionally agrees that all claims in respect of any such
action or proceeding may be heard and determined in such New York State court
or, to the extent permitted by law, in such federal court.  The Guarantor agrees
that a final judgment in any such action or proceeding shall be conclusive and
may be enforced in other jurisdictions by suit on the judgment or in any other
manner provided by law.  Nothing in this Section 5.11 shall affect any right
                                         ------------
that the Administrative Agent may otherwise have to bring any action or
proceeding relating to this Guaranty against the Guarantor or any of its
properties in the courts of any jurisdiction.  The Guarantor hereby irrevocably
and unconditionally waives, to the fullest extent it may legally and effectively
do so, any objection which it may now or hereafter have to the laying of venue
of any suit, action or proceeding arising out of or relating to this Guaranty in
any court referred to in this Section 5.11.  The Guarantor irrevocably waives,
                              ------------
to the fullest extent permitted by law, the defense of an inconvenient forum to
the maintenance of such action or proceeding in any such court. The Guarantor
irrevocably consents to service of process in the manner provided for notices in
Section 5.5.  Nothing in this Guaranty will affect the right of any party hereto
-----------
to serve process in any other manner permitted by law.

     Section 5.11  Waiver of Jury Trial.
                   ---------------------

     THE GUARANTOR HEREBY WAIVES, TO THE FULLEST EXTENT PERMITTED BY APPLICABLE
LAW, ANY RIGHT IT MAY HAVE TO A TRIAL BY JURY IN ANY

                                       9
<PAGE>

LEGAL PROCEEDING DIRECTLY OR INDIRECTLY ARISING OUT OF OR RELATING TO THIS
GUARANTY OR THE TRANSACTIONS CONTEMPLATED HEREBY (WHETHER BASED ON CONTRACT,
TORT OR ANY OTHER THEORY).

     Section 5.12  Construction.
                   -------------

     The Guarantor and the Administrative Agent each acknowledges that it has
had the benefit of legal counsel of its own choice and has been afforded an
opportunity to review this Guaranty with its legal counsel and that this
Guaranty shall be construed as if jointly drafted by the Guarantor and the
Administrative Agent.

     Section 5.13  Counterparts; Effectiveness.
                   ----------------------------

     This Guaranty and any amendments, waivers, consents, or supplements 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 of which counterparts together shall constitute but
one and the same instrument.  This Guaranty shall become effective upon the
execution of a counterpart hereof by each of the parties hereto.  Delivery of an
executed counterpart of a signature page to this Guaranty or to any amendments,
waivers, consents or supplements hereof or thereof by telecopier shall be as
effective as delivery of a manually executed counterpart thereof.


                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

                                       10
<PAGE>

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



                              FIBERNET TELECOM, INC.
                              as the Guarantor

                              By: /s/ Michael S. Liss
                                 --------------------------------
                                 Name:  Michael S. Liss
                                 Title: President

                              DEUTSCHE BANK AG NEW YORK
                                 BRANCH, as Administrative Agent

                              By: /s/ Jon D. Storck
                                 --------------------------------
                                 Name:  Jon D. Storck
                                 Title: Vice President

                              By: /s/ Alexander Richarz
                                 --------------------------------
                                 Name:  Alexander Richarz
                                 Title: Assistant Vice President

                                      S-1