| 9/2/2016 | Worcester Polytechnic | 37 | at | MIT | 34 | OT | @ NEF | |
| Western New England | 26 | at | Springfield | 10 | NEF | |||
| Morrisville | 0 | at | St Lawrence | 28 | E8 | |||
| 9/3/2016 | Hobart | 41 | at | Brockport State | 35 | @ E8 | ||
| Union NY | 9 | at | Ithaca | 14 | @ E8 | |||
| Rensselaer | 31 | at | Norwich | 17 | @ ECFC | |||
| 9/9/2016 | Worcester State | 7 | at | Worcester Polytechnic | 41 | MSCAC | ||
| 9/10/2016 | Merchant Marine | 31 | at | Coast Guard | 27 | @ NEF | ||
| Hobart | 42 | at | Endicott | 20 | @ NEF | |||
| Catholic | 27 | at | Rochester | 14 | ODC | |||
| Alfred | 33 | at | Rensselaer | 17 | E8 | |||
| St John Fisher | 35 | at | Springfield | 21 | E8 | |||
| Norwich | 0 | at | St Lawrence | 52 | ECFC | |||
| Western Connecticut | 13 | at | Union NY | 28 | MSCAC | |||
| 9/16/2016 | Merchant Marine | 16 | at | SUNY-Maritime | 20 | @ ECFC | ||
| 9/17/2016 | Rochester | 55 | at | Alfred State | 27 | @ D3Ind | ||
| St Lawrence | 38 | at | Endicott | 0 | @ NEF | |||
| Ithaca | 3 | at | Hobart | 23 | E8 | |||
| Rensselaer | 31 | at | MIT | 10 | @ NEF | |||
| Worcester Polytechnic | 40 | at | Norwich | 17 | @ ECFC | |||
| Mount Ida | 0 | at | Springfield | 32 | ECFC | |||
| Western New England | 32 | at | Union NY | 16 | NEF | |||
| 9/24/2016 | Union NY | 23 | at | Hobart | 27 | |||
| Rochester | 7 | at | Merchant Marine | 55 | ||||
| St Lawrence | 20 | at | Rensselaer | 14 | ||||
| Worcester Polytechnic | 23 | at | Springfield | 28 | ||||
| 10/1/2016 | Merchant Marine | 35 | at | Hobart | 38 | |||
| Rensselaer | 51 | at | Rochester | 13 | ||||
| Springfield | 14 | at | St Lawrence | 42 | ||||
| Union NY | 14 | at | Worcester Polytechnic | 21 | ||||
| 10/8/2016 | St Lawrence | 48 | at | Rochester | 13 | |||
| Hobart | 17 | at | Rensselaer | 21 | ||||
| Springfield | 17 | at | Union NY | 3 | ||||
| Merchant Marine | 45 | at | Worcester Polytechnic | 44 | ||||
| 10/15/2016 | Rensselaer | 13 | at | Merchant Marine | 16 | |||
| Rochester | 47 | at | Springfield | 70 | ||||
| 10/22/2016 | Springfield | 7 | at | Hobart | 12 | |||
| St Lawrence | 8 | at | Merchant Marine | 0 | ||||
| Worcester Polytechnic | 19 | at | Rensselaer | 7 | ||||
| Rochester | 15 | at | Union NY | 31 | ||||
| 10/29/2016 | Union NY | 14 | at | St Lawrence | 26 | |||
| Hobart | 35 | at | Worcester Polytechnic | 31 | ||||
| 11/5/2016 | Worcester Polytechnic | 37 | at | Rochester | 34 | |||
| Rensselaer | 7 | at | Springfield | 24 | ||||
| Hobart | 34 | at | St Lawrence | 18 | ||||
| Merchant Marine | 16 | at | Union NY | 42 | ||||
| 11/12/2016 | Rochester | 27 | at | Hobart | 56 | |||
| Springfield | 12 | at | Merchant Marine | 15 | ||||
| Union NY | 12 | at | Rensselaer | 21 | ||||
| St Lawrence | 28 | at | Worcester Polytechnic | 21 | ||||
| 11/19/2016 | Mount Union | 38 | at | Hobart | 21 | OAC | ||
| 11/20/2016 | Rensselaer | 38 | vs | SUNY-Maritime | 6 | Philadelphia PA | vs ECFC |