<PAGE>

   As filed with the Securities and Exchange Commission on November 15, 2000
                                             Registration No. 333-_______
================================================================================
                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C.  20549

                                   FORM S-8

                         REGISTRATION STATEMENT UNDER
                          THE SECURITIES ACT OF 1933

                             NETWORK ENGINES, INC.
            (Exact Name of Registrant as Specified in Its Charter)

               Delaware                                    04-3064173
    (State or Other Jurisdiction of                     (I.R.S. Employer
    Incorporation or Organization)                    Identification Number)

25 Dan Road, Canton, Massachusetts                          02021-2817
(Address of Principal Executive Offices)                    (Zip Code)

                     1999 STOCK INCENTIVE PLAN, AS AMENDED
                           (Full Title of the Plan)

                             Lawrence A. Genovesi
                             Network Engines, Inc.
                                  25 Dan Road
                       Canton, Massachusetts 02021-2817
                    (Name and Address of Agent for Service)

                                (781) 821-6042
         (Telephone Number, Including Area Code, of Agent for Service)

<TABLE>
<CAPTION>
===============================================================================================
                                      Proposed maximum    Proposed maximum       Amount of
Title of securities   Amount to be     offering price    aggregate offering     registration
to be registered      Registered(1)     per share(2)           price               fee
-----------------------------------------------------------------------------------------------
<S>                  <C>              <C>                <C>                    <C>
Common Stock
 $.01 par value          1,710,929        $15.125           $25,877,801.13         $6,831.74
===============================================================================================
</TABLE>

(1)  Pursuant to Rule 416(a) of the Securities Act, this Registration Statement
     shall also cover any additional shares of Common Stock which become
     issuable under the Plan being registered pursuant to this Registration
     Statement by reason of any stock dividend, stock split, recapitalization or
     any other similar transaction effected without the receipt of consideration
     which results in an increase in the number of the Registrant's outstanding
     shares of Common Stock.

(2)  Computed in accordance with Rule 457 (c) and (h) under the Securities Act
     of 1933, as amended, solely for the purpose of calculating the registration
     fee, based upon the average of the high and low prices of the Common Stock
     on the Nasdaq National Market on November 10, 2000.
<PAGE>

PART I.  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

The information required by Part I is included in documents sent or given to
participants in the Registrant's 1999 Stock Incentive Plan, as amended, pursuant
to Rule 428(b)(1) of the Securities Act of 1933, as amended (the "Securities
Act").

PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Statement of Incorporation by Reference

There are incorporated herein by reference (i) the Registration Statement on
Form S-8, File No. 333-41374, filed by the Registrant on July 13, 2000, relating
to the Registrant's 1999 Stock Incentive Plan, as amended, 2000 Employee Stock
Purchase Plan and 2000 Director Stock Option Plan, (ii) the prospectus filed
pursuant to Rule 424(b) of the Securities Act relating to the Registration
Statement on Form S-1 (Registration No. 333-34286) (the "Form S-1") of Network
Engines, Inc. (the "Registrant"), containing audited financial statements for
the Registrant's latest fiscal year for which such statements have been filed by
the Registrant with the Securities and Exchange Commission, (iii) all other
reports filed by the Registrant pursuant to Section 13(a) or 15(d) of the
Securities Exchange Act of 1934, as amended (the "Exchange Act"), since the end
of the fiscal year covered by the document referred to in (ii) above and (iv)
the description of the common stock, par value $0.01 per share, of the
Registrant contained in the Registrant's registration statement filed under the
Exchange Act, including any amendment or report filed for the purpose of
updating such description.

All documents subsequently filed by the Registrant pursuant to Sections 13(a),
13(c), 14 and 15(d) of the Exchange Act, prior to the filing of a post-effective
amendment which indicates that all securities offered have been sold or which
deregisters all securities then remaining unsold, shall be deemed to be
incorporated by reference in this Registration Statement and to be a part hereof
from the date of filing of such documents.

                                      II-1
<PAGE>

                                  SIGNATURES

Pursuant to the requirements of the Securities Act, the Registrant certifies
that it has reasonable grounds to believe that it meets all of the requirements
for filing on Form S-8 and has duly caused this Registration Statement to be
signed on its behalf by the undersigned, thereunto duly authorized, in Canton,
Massachusetts on November 15, 2000.

                                        NETWORK ENGINES, INC.

                                        By: /s/ Lawrence A. Genovesi
                                            ------------------------
                                        Lawrence A. Genovesi
                                        Chairman of the Board, President,
                                        Chief Executive Officer and Chief
                                        Technology Officer


                       POWER OF ATTORNEY AND SIGNATURES

We, the undersigned officers and directors of Network Engines, Inc., hereby
severally constitute and appoint Lawrence A. Genovesi, Douglas G. Bryant and
Philip P. Rossetti and each of them singly, our true and lawful attorneys with
full power to them, and each of them singly, to sign for us and in our names in
the capacities indicated below, the Registration Statement on Form S-8 filed
herewith and any and all subsequent amendments to said Registration Statement,
and generally to do all such things in our names and behalf in our capacities as
officers and directors to enable Network Engines Inc. to comply with all
requirements of the Securities and Exchange Commission, hereby ratifying and
confirming our signatures as they may be signed by said attorneys, or any of
them, to said Registration Statement and any and all amendments thereto.

Pursuant to the requirements of the Securities Act, this Registration Statement
has been signed by the following persons in the capacities and on the dates
indicated.


<TABLE>
<CAPTION>
              Signature                                  Title                          Date
<S>                                        <C>                                    <C>
       /s/ Lawrence A. Genovesi
--------------------------------------
          Lawrence A. Genovesi             Chairman of the Board, President,      November 15, 2000
                                           Chief Executive Officer and Chief
                                           Technology Officer

       /s/ Douglas G. Bryant
--------------------------------------
          Douglas G. Bryant                Vice President of Administration,      November 15, 2000
                                           Chief Financial Officer,
                                           Treasurer and Secretary
                                           (Principal Financial and
                                           Accounting Officer)
</TABLE>

                                      II-2
<PAGE>

<TABLE>
<S>                                        <C>                                    <C>
       /s/ John A. Blaeser
--------------------------------------
          John A. Blaeser                  Director                               November 9, 2000

       /s/ Lawrence Kernan
--------------------------------------
          Lawrence Kernan                  Director                               November 10, 2000

       /s/ Dennis A. Kirshy
--------------------------------------
          Dennis A. Kirshy                 Director                               November 14, 2000

       /s/ Frank M. Polestra
--------------------------------------
          Frank M. Polestra                Director                               November 15, 2000

       /s/ Michael H. Shanahan
--------------------------------------
          Michael H. Shanahan              Director                               November 15, 2000

       /s/ Robert M. Wadsworth
--------------------------------------
          Robert M. Wadsworth              Director                               November 15, 2000
</TABLE>


                                      II-3
<PAGE>

                                 EXHIBIT INDEX

Exhibit
Number                   Description
------                   -----------

  5         Opinion of Hale and Dorr LLP

 23.1       Consent of Hale and Dorr LLP (included in Exhibit 5)

 23.2       Consent of PricewaterhouseCoopers LLP, independent accountants

 24         Power of Attorney (included in the signature pages of this
            Registration Statement)
[{"type": "S-8", "sequence": "1", "filename": "0001.txt", "description": "FORM S-8", "secsgml_size_bytes": 9679}]
{"company-data": {"conformed-name": "NETWORK ENGINES INC", "cik": "0001110903", "assigned-sic": "7372", "state-of-incorporation": "DE", "fiscal-year-end": "0930"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-49978", "film-number": "770287"}, "business-address": {"street1": "61 PLEASANT STREET", "city": "RANDOLPH", "state": "MA", "zip": "02368", "phone": "7819614400"}}
As filed with the Securities and Exchange Commission on November 15, 2000
                                             Registration No. 333-_______
================================================================================
                      SECURITIES AND EXCHANGE COMMISSION
                            Washington, D.C.  20549

                                   FORM S-8

                         REGISTRATION STATEMENT UNDER
                          THE SECURITIES ACT OF 1933

                             NETWORK ENGINES, INC.
            (Exact Name of Registrant as Specified in Its Charter)

               Delaware                                    04-3064173
    (State or Other Jurisdiction of                     (I.R.S. Employer
    Incorporation or Organization)                    Identification Number)

25 Dan Road, Canton, Massachusetts                          02021-2817
(Address of Principal Executive Offices)                    (Zip Code)

                     1999 STOCK INCENTIVE PLAN, AS AMENDED
                           (Full Title of the Plan)

                             Lawrence A. Genovesi
                             Network Engines, Inc.
                                  25 Dan Road
                       Canton, Massachusetts 02021-2817
                    (Name and Address of Agent for Service)

                                (781) 821-6042
         (Telephone Number, Including Area Code, of Agent for Service)
===============================================================================================
                                      Proposed maximum    Proposed maximum       Amount of
Title of securities   Amount to be     offering price    aggregate offering     registration
to be registered      Registered(1)     per share(2)           price               fee
-----------------------------------------------------------------------------------------------
Common Stock
 $.01 par value          1,710,929        $15.125           $25,877,801.13         $6,831.74
===============================================================================================
(1)  Pursuant to Rule 416(a) of the Securities Act, this Registration Statement
     shall also cover any additional shares of Common Stock which become
     issuable under the Plan being registered pursuant to this Registration
     Statement by reason of any stock dividend, stock split, recapitalization or
     any other similar transaction effected without the receipt of consideration
     which results in an increase in the number of the Registrant's outstanding
     shares of Common Stock.

(2)  Computed in accordance with Rule 457 (c) and (h) under the Securities Act
     of 1933, as amended, solely for the purpose of calculating the registration
     fee, based upon the average of the high and low prices of the Common Stock
     on the Nasdaq National Market on November 10, 2000.
PART I.  INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS

The information required by Part I is included in documents sent or given to
participants in the Registrant's 1999 Stock Incentive Plan, as amended, pursuant
to Rule 428(b)(1) of the Securities Act of 1933, as amended (the "Securities
Act").

PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Statement of Incorporation by Reference

There are incorporated herein by reference (i) the Registration Statement on
Form S-8, File No. 333-41374, filed by the Registrant on July 13, 2000, relating
to the Registrant's 1999 Stock Incentive Plan, as amended, 2000 Employee Stock
Purchase Plan and 2000 Director Stock Option Plan, (ii) the prospectus filed
pursuant to Rule 424(b) of the Securities Act relating to the Registration
Statement on Form S-1 (Registration No. 333-34286) (the "Form S-1") of Network
Engines, Inc. (the "Registrant"), containing audited financial statements for
the Registrant's latest fiscal year for which such statements have been filed by
the Registrant with the Securities and Exchange Commission, (iii) all other
reports filed by the Registrant pursuant to Section 13(a) or 15(d) of the
Securities Exchange Act of 1934, as amended (the "Exchange Act"), since the end
of the fiscal year covered by the document referred to in (ii) above and (iv)
the description of the common stock, par value $0.01 per share, of the
Registrant contained in the Registrant's registration statement filed under the
Exchange Act, including any amendment or report filed for the purpose of
updating such description.

All documents subsequently filed by the Registrant pursuant to Sections 13(a),
13(c), 14 and 15(d) of the Exchange Act, prior to the filing of a post-effective
amendment which indicates that all securities offered have been sold or which
deregisters all securities then remaining unsold, shall be deemed to be
incorporated by reference in this Registration Statement and to be a part hereof
from the date of filing of such documents.

                                      II-1
SIGNATURES

Pursuant to the requirements of the Securities Act, the Registrant certifies
that it has reasonable grounds to believe that it meets all of the requirements
for filing on Form S-8 and has duly caused this Registration Statement to be
signed on its behalf by the undersigned, thereunto duly authorized, in Canton,
Massachusetts on November 15, 2000.

                                        NETWORK ENGINES, INC.

                                        By: /s/ Lawrence A. Genovesi
                                            ------------------------
                                        Lawrence A. Genovesi
                                        Chairman of the Board, President,
                                        Chief Executive Officer and Chief
                                        Technology Officer

                       POWER OF ATTORNEY AND SIGNATURES

We, the undersigned officers and directors of Network Engines, Inc., hereby
severally constitute and appoint Lawrence A. Genovesi, Douglas G. Bryant and
Philip P. Rossetti and each of them singly, our true and lawful attorneys with
full power to them, and each of them singly, to sign for us and in our names in
the capacities indicated below, the Registration Statement on Form S-8 filed
herewith and any and all subsequent amendments to said Registration Statement,
and generally to do all such things in our names and behalf in our capacities as
officers and directors to enable Network Engines Inc. to comply with all
requirements of the Securities and Exchange Commission, hereby ratifying and
confirming our signatures as they may be signed by said attorneys, or any of
them, to said Registration Statement and any and all amendments thereto.

Pursuant to the requirements of the Securities Act, this Registration Statement
has been signed by the following persons in the capacities and on the dates
indicated.
Signature                                  Title                          Date
/s/ Lawrence A. Genovesi
--------------------------------------
          Lawrence A. Genovesi             Chairman of the Board, President,      November 15, 2000
                                           Chief Executive Officer and Chief
                                           Technology Officer

       /s/ Douglas G. Bryant
--------------------------------------
          Douglas G. Bryant                Vice President of Administration,      November 15, 2000
                                           Chief Financial Officer,
                                           Treasurer and Secretary
                                           (Principal Financial and
                                           Accounting Officer)
II-2
/s/ John A. Blaeser
--------------------------------------
          John A. Blaeser                  Director                               November 9, 2000

       /s/ Lawrence Kernan
--------------------------------------
          Lawrence Kernan                  Director                               November 10, 2000

       /s/ Dennis A. Kirshy
--------------------------------------
          Dennis A. Kirshy                 Director                               November 14, 2000

       /s/ Frank M. Polestra
--------------------------------------
          Frank M. Polestra                Director                               November 15, 2000

       /s/ Michael H. Shanahan
--------------------------------------
          Michael H. Shanahan              Director                               November 15, 2000

       /s/ Robert M. Wadsworth
--------------------------------------
          Robert M. Wadsworth              Director                               November 15, 2000
II-3
EXHIBIT INDEX

Exhibit
Number                   Description
------                   -----------

  5         Opinion of Hale and Dorr LLP

 23.1       Consent of Hale and Dorr LLP (included in Exhibit 5)

 23.2       Consent of PricewaterhouseCoopers LLP, independent accountants

 24         Power of Attorney (included in the signature pages of this
            Registration Statement)