| 9/1/2012 | Cortland | 31 | at | Buffalo State | 49 | vs NJAC | ||
| Salisbury | 40 | at | Christopher Newport | 16 | @ USASC | |||
| Geneva | 53 | at | Frostburg State | 56 | vs TPAC | |||
| Hartwick | 55 | at | Husson | 14 | @ ECFC | |||
| Ithaca | 24 | at | Moravian | 0 | @ Cen | |||
| Thomas More | 7 | at | St John Fisher | 13 | OT | vs TPAC | ||
| St Lawrence | 7 | at | Utica | 40 | vs LL | |||
| 9/8/2012 | Buffalo State | 24 | at | Brockport State | 38 | @ NJAC | ||
| Morrisville | 7 | at | Hartwick | 36 | vs NJAC | |||
| Alfred | 6 | at | Rensselaer | 24 | @ LL | |||
| Wesley | 17 | at | Salisbury | 7 | vs D3Ind | |||
| Utica | 45 | at | Union NY | 17 | @ LL | |||
| St John Fisher | 28 | at | Washington & Jefferson | 24 | @ TPAC | |||
| Frostburg State | 7 | at | Waynesburg | 21 | @ TPAC | |||
| 9/15/2012 | Frostburg State | 17 | at | Case Western Reserve | 16 | @ UAA | ||
| Becker | 41 | at | Hartwick | 53 | vs ECFC | |||
| Union NY | 24 | at | Ithaca | 27 | vs LL | |||
| North Carolina Wesleyan | 6 | at | Salisbury | 69 | vs USASC | |||
| Rochester | 16 | at | St John Fisher | 20 | vs LL | |||
| Alfred | 28 | at | St Lawrence | 7 | @ LL | |||
| Hobart | 45 | at | Utica | 26 | vs LL | |||
| Buffalo State | 7 | at | Wisconsin-Whitewater | 6 | @ WIAC | |||
| 9/22/2012 | Alfred | 40 | at | Buffalo State | 17 | |||
| Ithaca | 40 | at | Frostburg State | 21 | ||||
| Hartwick | 13 | at | St John Fisher | 43 | ||||
| 9/29/2012 | Salisbury | 20 | at | Buffalo State | 7 | |||
| Frostburg State | 28 | at | Hartwick | 26 | ||||
| Utica | 22 | at | Ithaca | 40 | ||||
| 10/6/2012 | Ithaca | 7 | at | Alfred | 31 | |||
| Utica | 51 | at | Buffalo State | 44 | ||||
| Salisbury | 28 | at | St John Fisher | 17 | ||||
| 10/13/2012 | St John Fisher | 13 | at | Alfred | 26 | |||
| Buffalo State | 21 | at | Ithaca | 14 | ||||
| Hartwick | 7 | at | Salisbury | 37 | ||||
| Frostburg State | 0 | at | Utica | 41 | ||||
| 10/20/2012 | Buffalo State | 22 | at | Frostburg State | 7 | |||
| Utica | 43 | at | Hartwick | 7 | ||||
| Alfred | 21 | at | Salisbury | 24 | ||||
| Ithaca | 17 | at | St John Fisher | 21 | ||||
| 10/27/2012 | Hartwick | 24 | at | Buffalo State | 27 | |||
| St John Fisher | 21 | at | Frostburg State | 0 | ||||
| Salisbury | 14 | at | Ithaca | 21 | ||||
| Alfred | 7 | at | Utica | 31 | ||||
| 11/3/2012 | Frostburg State | 14 | at | Alfred | 40 | |||
| Hartwick | 7 | at | Ithaca | 28 | ||||
| Utica | 23 | at | Salisbury | 63 | ||||
| Buffalo State | 17 | at | St John Fisher | 9 | ||||
| 11/10/2012 | Ithaca | 10 | at | Cortland | 16 | @ NJAC | ||
| Salisbury | 48 | at | Frostburg State | 2 | ||||
| Alfred | 30 | at | Hartwick | 13 | ||||
| St John Fisher | 55 | at | Utica | 20 | ||||
| 11/17/2012 | Rowan | 9 | at | Salisbury | 17 | Div 3 Playoffs 1st Round | vs NJAC | |
| Alfred | 8 | at | Springfield | 31 | @ LL | |||
| Castleton State | 7 | at | St John Fisher | 63 | ECAC Northwest Bowl | vs ECFC | ||
| 11/24/2012 | Salisbury | 7 | a | Widener | 28 | D3 Playoffs Round 2 | @ MidAC |