| 9/3/2016 | West Virginia Wesleyan (4-7,4-6) | 12 | at | Shepherd | 27 | | | |
| 9/8/2016 | Shepherd | 38 | at | Charleston WV (3-8,3-7) | 22 | | | |
| 9/17/2016 | Virginia-Wise (6-5,5-5) | 13 | at | Shepherd | 64 | | | |
| 9/24/2016 | Shepherd | 38 | at | Notre Dame OH (9-2,8-2) | 17 | | | |
| 10/8/2016 | Glenville State (5-6,5-5) | 7 | at | Shepherd | 38 | | | |
| 10/15/2016 | Shepherd | 70 | at | West Virginia State (3-8,3-7) | 24 | | | |
| 10/22/2016 | Concord (2-9,2-8) | 7 | at | Shepherd | 21 | | | |
| 10/29/2016 | Shepherd | 38 | at | West Liberty (4-7,4-6) | 27 | | | |
| 11/5/2016 | Fairmont State (10-2,9-1) | 17 | at | Shepherd | 27 | | | |
| 11/12/2016 | Shepherd | 38 | at | Urbana (3-8,2-8) | 14 | | | |
| 11/19/2016 | Assumption (9-3) | 31 | at | Shepherd | 48 | | | NE10 |
| 11/26/2016 | Shepherd | 40 | at | LIU Post (12-1) | 21 | | | at NE10 |
| 12/3/2016 | Shepherd | 41 | at | California PA (11-1) | 30 | | D2 Quarterfinal | at PSAC |
| 12/10/2016 | North Alabama (11-2) | 23 | at | Shepherd | 13 | | D2 Semifinal | GSC |