| 9/1/2016 | Shorter | 0 | at | Chattanooga | 66 | @ SoCon (1AA) | ||
| Kentucky Wesleyan | 29 | at | Delta State | 50 | D2Ind | |||
| North Alabama | 12 | at | Jacksonville State | 31 | @ OVC (1AA) | |||
| West Alabama | 23 | at | North Greenville | 24 | @ D2Ind | |||
| 9/3/2016 | West Florida | 45 | at | Ave Maria | 0 | @ Sun (NAIA) | ||
| Point | 16 | at | Mississippi College | 28 | Sun (NAIA) | |||
| Florida Tech | 42 | at | Newberry | 28 | @ SAC | |||
| Albany State GA | 7 | at | Valdosta State | 16 | SIAC | |||
| Catawba | 3 | at | West Georgia | 23 | SAC | |||
| 9/10/2016 | Texas A&M-Commerce | 40 | at | Delta State | 28 | LSC | ||
| Mississippi College | 0 | at | Florida Tech | 41 | ||||
| Shorter | 21 | at | Mars Hill | 28 | OT | @ SAC | ||
| West Georgia | 29 | at | Miles | 0 | @ SIAC | |||
| West Alabama | 24 | at | Stephen F. Austin | 30 | @ SLC (1AA) | |||
| Missouri S&T | 28 | at | West Florida | 45 | GLV | |||
| 9/17/2016 | West Florida | 28 | at | Chowan | 35 | @ CIAA | ||
| West Alabama | 38 | at | Mississippi College | 13 | ||||
| Valdosta State | 19 | at | North Alabama | 44 | ||||
| Florida Tech | 40 | at | Shorter | 0 | ||||
| Delta State | 24 | at | West Georgia | 34 | ||||
| 9/24/2016 | West Georgia | 27 | at | Albany State GA | 23 | @ SIAC | ||
| Shorter | 7 | at | Delta State | 47 | ||||
| Cumberland TN | 26 | at | Mississippi College | 27 | MSC (NAIA) | |||
| Florida Tech | 28 | at | Presbyterian | 7 | @ BigS (1AA) | |||
| West Florida | 28 | at | Valdosta State | 40 | ||||
| North Alabama | 45 | at | West Alabama | 7 | ||||
| 9/29/2016 | Mississippi College | 31 | at | Delta State | 61 | |||
| West Alabama | 43 | at | Shorter | 28 | ||||
| 10/1/2016 | West Georgia | 23 | at | North Alabama | 24 | |||
| Kentucky State | 10 | vs | Valdosta State | 48 | Waycross GA | vs SIAC | ||
| Florida Tech | 39 | at | West Florida | 42 | ||||
| 10/6/2016 | Clark Atlanta | 27 | at | Shorter | 23 | SIAC | ||
| 10/8/2016 | North Alabama | vs | Florida Tech | Cancelled WX | ||||
| West Florida | 42 | at | Mississippi College | 28 | ||||
| West Georgia | 27 | at | Valdosta State | 38 | ||||
| Delta State | 42 | at | West Alabama | 54 | ||||
| 10/15/2016 | West Florida | 51 | at | Delta State | 55 | |||
| Fort Valley State | 14 | at | Florida Tech | 48 | SIAC | |||
| Valdosta State | 42 | at | Mississippi College | 41 | ||||
| Shorter | 0 | at | North Alabama | 45 | ||||
| West Alabama | 31 | at | West Georgia | 7 | ||||
| 10/22/2016 | North Greenville | 21 | at | North Alabama | 52 | D2Ind | ||
| Delta State | 27 | at | Valdosta State | 56 | ||||
| Florida Tech | 35 | at | West Alabama | 45 | ||||
| Shorter | 0 | at | West Florida | 36 | ||||
| Mississippi College | 23 | at | West Georgia | 31 | ||||
| 10/29/2016 | North Alabama | 49 | at | Delta State | 19 | |||
| Valdosta State | 20 | at | Florida Tech | 38 | ||||
| West Georgia | 44 | at | Shorter | 0 | ||||
| West Alabama | 45 | at | West Florida | 21 | ||||
| 11/5/2016 | West Florida | 3 | at | North Alabama | 51 | |||
| Mississippi College | 32 | at | Shorter | 0 | ||||
| Valdosta State | 37 | at | West Alabama | 22 | ||||
| Florida Tech | 45 | at | West Georgia | 21 | ||||
| 11/12/2016 | Delta State | 16 | at | Florida Tech | 42 | |||
| North Alabama | 42 | at | Mississippi College | 7 | ||||
| Shorter | 0 | at | Valdosta State | 44 | ||||
| Malone | 7 | at | West Alabama | 56 | GLIAC | |||
| West Georgia | 69 | at | West Florida | 0 | ||||
| 11/19/2016 | North Greenville | 27 | at | Florida Tech | 13 | D2Ind | ||
| UNC Pembroke | 24 | at | Valdosta State | 21 | D2Ind | |||
| 11/26/2016 | UNC Pembroke | 17 | at | North Alabama | 41 | D2Ind | ||
| 12/3/2016 | North Greenville | 0 | at | North Alabama | 38 | D2 Quarterfinal | D2Ind | |
| 12/10/2016 | North Alabama | 23 | at | Shepherd | 13 | D2 Semifinal | @ MtnE | |
| 12/17/2016 | North Alabama | 3 | vs | Northwest Missouri State | 29 | D2 Championship (Kansas City KS) | vs MAIAA |