9/1/2016 | Montana State | 17 | at | Idaho | 20 | | | BSky (1AA) |
| Appalachian State | 13 | at | Tennessee | 20 | OT | | @ SEC |
9/2/2016 | Toledo | 31 | at | Arkansas State | 10 | | | MAC |
| Ball State | 31 | at | Georgia State | 21 | | | MAC |
9/3/2016 | Savannah State | 0 | at | Georgia Southern | 54 | | | MEAC (1AA) |
| Boise State | 45 | at | UL Lafayette | 10 | | | MW |
| Southern | 21 | at | UL Monroe | 38 | | | SWAC (1AA) |
| South Alabama | 21 | at | Mississippi State | 20 | | | @ SEC |
| Texas State | 56 | at | Ohio | 54 | OT | | @ MAC |
| Austin Peay | 17 | at | Troy | 57 | | | OVC (1AA) |
| New Mexico State | 22 | at | UTEP | 38 | | | @ CUSA |
9/10/2016 | Georgia State | 14 | at | Air Force | 48 | | | @ MW |
| Old Dominion | 7 | at | Appalachian State | 31 | | | CUSA |
| Arkansas State | 14 | at | Auburn | 51 | | | @ SEC |
| Troy | 24 | at | Clemson | 30 | | | @ ACC |
| McNeese State | 22 | at | UL Lafayette | 30 | | | SLC (1AA) |
| New Mexico | 31 | at | New Mexico State | 32 | | | MW |
| UL Monroe | 17 | at | Oklahoma | 59 | | | @ B12 |
| Georgia Southern | 24 | at | South Alabama | 9 | | | |
| Idaho | 14 | at | Washington | 59 | | | @ P12 |
9/16/2016 | Arkansas State | 20 | at | Utah State | 34 | | | @ MW |
9/17/2016 | Miami-Florida | 45 | at | Appalachian State | 10 | | | ACC |
| Texas State | 3 | at | Arkansas | 42 | | | @ SEC |
| UL Monroe | 21 | at | Georgia Southern | 23 | | | |
| New Mexico State | 42 | at | Kentucky | 62 | | | @ SEC |
| South Alabama | 23 | at | UL Lafayette | 28 | | | |
| Troy | 37 | at | Southern Miss | 31 | | | @ CUSA |
| Idaho | 6 | at | Washington State | 56 | | | @ P12 |
| Georgia State | 17 | at | Wisconsin | 23 | | | @ B10 |
9/24/2016 | Appalachian State | 45 | at | Akron | 38 | | | @ MAC |
| Central Arkansas | 28 | at | Arkansas State | 23 | | | SLC (1AA) |
| Nicholls State | 40 | at | South Alabama | 41 | OT | | SLC (1AA) |
| Houston | 64 | at | Texas State | 3 | | | AAC |
| New Mexico State | 6 | at | Troy | 52 | | | |
| UL Lafayette | 39 | at | Tulane | 41 | 4OT | | @ AAC |
| Idaho | 33 | at | UNLV | 30 | OT | | @ MW |
| Georgia Southern | 31 | at | Western Michigan | 49 | | | @ MAC |
10/1/2016 | Georgia State | 3 | at | Appalachian State | 17 | | | |
| UL Monroe | 7 | at | Auburn | 58 | | | @ SEC |
| Troy | 34 | at | Idaho | 13 | | | |
| UL Lafayette | 31 | at | New Mexico State | 37 | 2OT | | |
| San Diego State | 24 | at | South Alabama | 42 | | | MW |
| Incarnate Word | 17 | at | Texas State | 48 | | | SLC (1AA) |
10/5/2016 | Georgia Southern | 26 | at | Arkansas State | 27 | | | |
10/8/2016 | Texas State | 21 | at | Georgia State | 41 | | | |
| Idaho | 34 | at | UL Monroe | 31 | | | |
10/12/2016 | Appalachian State | 24 | at | UL Lafayette | 0 | | | |
10/15/2016 | South Alabama | 7 | at | Arkansas State | 17 | | | |
| Georgia Southern | 24 | at | Georgia Tech | 35 | | | @ ACC |
| New Mexico State | 23 | at | Idaho | 55 | | | |
| Texas State | 34 | at | UL Monroe | 40 | | | |
| Georgia State | 21 | at | Troy | 31 | | | |
10/20/2016 | Troy | 28 | at | South Alabama | 21 | | | |
10/22/2016 | Idaho | 19 | at | Appalachian State | 37 | | | |
| Tennessee-Martin | 6 | at | Georgia State | 31 | | | OVC (1AA) |
| UL Monroe | 17 | at | New Mexico | 59 | | | @ MW |
| Georgia Southern | 22 | at | New Mexico State | 19 | | | |
| UL Lafayette | 27 | at | Texas State | 3 | | | |
10/27/2016 | Appalachian State | 34 | at | Georgia Southern | 10 | | | |
10/29/2016 | UL Monroe | 10 | at | Arkansas State | 51 | | | |
| Georgia State | 10 | at | South Alabama | 13 | | | |
| New Mexico State | 10 | at | Texas A&M | 52 | | | @ SEC |
11/3/2016 | Arkansas State | 31 | at | Georgia State | 16 | | | |
11/5/2016 | Texas State | 10 | at | Appalachian State | 35 | | | |
| Idaho | 23 | at | UL Lafayette | 13 | | | |
| South Alabama | 35 | at | UL Monroe | 42 | OT | | |
| Georgia Southern | 27 | at | Mississippi | 37 | | | @ SEC |
| Massachusetts | 31 | at | Troy | 52 | | | MAC |
11/10/2016 | UL Lafayette | 33 | at | Georgia Southern | 26 | | | |
11/12/2016 | New Mexico State | 22 | at | Arkansas State | 41 | | | |
| UL Monroe | 37 | at | Georgia State | 23 | | | |
| Idaho | 47 | at | Texas State | 14 | | | |
| Appalachian State | 24 | at | Troy | 28 | | | |
11/17/2016 | Arkansas State | 35 | at | Troy | 3 | | | |
11/19/2016 | UL Monroe | 17 | at | Appalachian State | 42 | | | |
| UL Lafayette | 21 | at | Georgia | 35 | | | @ SEC |
| Georgia Southern | 24 | at | Georgia State | 30 | | | |
| Texas State | 10 | at | New Mexico State | 50 | | | |
| Presbyterian | 7 | at | South Alabama | 31 | | | BigS (1AA) |
11/26/2016 | South Alabama | 31 | at | Idaho | 38 | | | |
| Arkansas State | 19 | at | UL Lafayette | 24 | | | |
| Appalachian State | 37 | at | New Mexico State | 7 | | | |
| Troy | 40 | at | Texas State | 7 | | | |
12/3/2016 | Troy | 24 | at | Georgia Southern | 28 | | | |
| Georgia State | 12 | at | Idaho | 37 | | | |
| UL Lafayette | 30 | at | UL Monroe | 3 | | | |
| New Mexico State | 28 | at | South Alabama | 35 | | | |
| Arkansas State | 36 | at | Texas State | 14 | | | |
12/17/2016 | UCF | 13 | vs | Arkansas State | 31 | | | vs AAC |
| Southern Miss | 28 | vs | UL Lafayette | 21 | | New Orleans Bowl | vs CUSA |
| Appalachian State | 31 | vs | Toledo | 28 | | Camellia Bowl (Montgomery AL) | vs MAC |
12/22/2016 | Idaho | 61 | vs | Colorado State | 50 | | Famous Idaho Potato Bowl (Boise ID) | vs MW |
12/23/2016 | Ohio | 23 | vs | Troy | 28 | | Dollar General Bowl (Mobile AL) | vs MAC |
12/30/2016 | South Alabama | 21 | vs | Air Force | 45 | | Arizona Bowl (Tuscon AZ) | vs MW |