| 9/1/2016 | Indiana | 34 | at | Florida Intl | 13 | B10 | ||
| UNC-Charlotte | 14 | at | Louisville | 70 | @ ACC | |||
| Rice | 14 | at | Western Kentucky | 46 | ||||
| 9/3/2016 | Louisiana Tech | 20 | at | Arkansas | 21 | @ SEC | ||
| Southern Illinois | 30 | at | Florida Atlantic | 38 | MVC (1AA) | |||
| Southern Miss | 44 | at | Kentucky | 35 | @ SEC | |||
| Alabama A&M | 0 | at | Middle Tenn State | 55 | SWAC (1AA) | |||
| SMU | 34 | at | North Texas | 21 | AAC | |||
| Alabama State | 13 | at | Texas-San Antonio | 26 | SWAC (1AA) | |||
| New Mexico State | 22 | at | UTEP | 38 | SBC | |||
| 9/4/2016 | Hampton | 21 | at | Old Dominion | 54 | MEAC (1AA) | ||
| 9/9/2016 | Maryland | 41 | at | Florida Intl | 14 | B10 | ||
| 9/10/2016 | Western Kentucky | 10 | at | Alabama | 38 | @ SEC | ||
| Old Dominion | 7 | at | Appalachian State | 31 | @ SBC | |||
| Rice | 14 | at | Army | 31 | @ Ind | |||
| Texas-San Antonio | 14 | at | Colorado State | 23 | @ MW | |||
| South Carolina State | 24 | at | Louisiana Tech | 53 | MEAC (1AA) | |||
| Morgan State | 0 | at | Marshall | 62 | MEAC (1AA) | |||
| Florida Atlantic | 10 | at | Miami-Florida | 38 | @ ACC | |||
| Bethune-Cookman | 20 | at | North Texas | 41 | MEAC (1AA) | |||
| Savannah State | 0 | at | Southern Miss | 56 | MEAC (1AA) | |||
| UTEP | 7 | at | Texas | 41 | @ B12 | |||
| Elon | 14 | at | UNC-Charlotte | 47 | CAAF (1AA) | |||
| Middle Tenn State | 24 | at | Vanderbilt | 47 | @ SEC | |||
| 9/16/2016 | Baylor | 38 | at | Rice | 10 | B12 | ||
| Arizona State | 32 | at | Texas-San Antonio | 28 | P12 | |||
| 9/17/2016 | Middle Tenn State | 41 | at | Bowling Green | 21 | @ MAC | ||
| North Texas | 0 | at | Florida | 32 | @ SEC | |||
| Florida Atlantic | 7 | at | Kansas State | 63 | @ B12 | |||
| Akron | 65 | at | Marshall | 38 | MAC | |||
| Florida Intl | 13 | at | Massachusetts | 21 | @ MAC | |||
| Western Kentucky | 31 | at | Miami-Ohio | 24 | @ MAC | |||
| Old Dominion | 22 | at | North Carolina State | 49 | @ ACC | |||
| Troy | 37 | at | Southern Miss | 31 | SBC | |||
| Louisiana Tech | 45 | at | Texas Tech | 59 | @ B12 | |||
| Eastern Michigan | 37 | at | UNC-Charlotte | 19 | MAC | |||
| Army | 66 | at | UTEP | 14 | Ind | |||
| 9/24/2016 | Ball State | 31 | at | Florida Atlantic | 27 | MAC | ||
| UCF | 53 | at | Florida Intl | 14 | AAC | |||
| Louisville | 59 | at | Marshall | 28 | ACC | |||
| Louisiana Tech | 34 | at | Middle Tenn State | 38 | ||||
| Texas-San Antonio | 19 | at | Old Dominion | 33 | ||||
| North Texas | 42 | at | Rice | 35 | 2OT | |||
| UNC-Charlotte | 20 | at | Temple | 48 | @ AAC | |||
| Southern Miss | 34 | at | UTEP | 7 | ||||
| Vanderbilt | 31 | at | Western Kentucky | 30 | OT | SEC | ||
| 10/1/2016 | Florida Atlantic | 31 | at | Florida Intl | 33 | |||
| UTEP | 7 | at | Louisiana Tech | 28 | ||||
| Middle Tenn State | 30 | at | North Texas | 13 | ||||
| Marshall | 27 | at | Pittsburgh | 43 | @ ACC | |||
| Rice | 28 | at | Southern Miss | 44 | ||||
| Old Dominion | 52 | at | UNC-Charlotte | 17 | ||||
| Houston Baptist | 3 | at | Western Kentucky | 50 | SLC (1AA) | |||
| 10/6/2016 | Western Kentucky | 52 | at | Louisiana Tech | 55 | |||
| 10/7/2016 | Massachusetts | 16 | at | Old Dominion | 36 | MAC | ||
| 10/8/2016 | Marshall | 21 | at | North Texas | 38 | |||
| Southern Miss | 32 | at | Texas-San Antonio | 55 | ||||
| Florida Intl | 35 | at | UTEP | 21 | ||||
| 10/9/2016 | UNC-Charlotte | 28 | at | Florida Atlantic | 23 | |||
| 10/15/2016 | Southern Miss | 10 | at | LSU | 45 | @ SEC | ||
| Florida Atlantic | 21 | at | Marshall | 27 | ||||
| Louisiana Tech | 56 | vs | Massachusetts | 28 | Foxboro MA | vs MAC | ||
| Western Kentucky | 44 | at | Middle Tenn State | 43 | 2OT | |||
| Texas-San Antonio | 14 | at | Rice | 13 | ||||
| Florida Intl | 27 | at | UNC-Charlotte | 26 | ||||
| 10/22/2016 | North Texas | 35 | at | Army | 18 | @ Ind | ||
| Louisiana Tech | 44 | at | Florida Intl | 24 | ||||
| UNC-Charlotte | 27 | at | Marshall | 24 | ||||
| Middle Tenn State | 51 | at | Missouri | 45 | @ SEC | |||
| Prairie View | 44 | at | Rice | 65 | SWAC (1AA) | |||
| UTEP | 52 | at | Texas-San Antonio | 49 | 5OT | |||
| Old Dominion | 24 | at | Western Kentucky | 59 | ||||
| 10/29/2016 | Western Kentucky | 52 | at | Florida Atlantic | 3 | |||
| Middle Tenn State | 42 | at | Florida Intl | 35 | ||||
| Rice | 16 | at | Louisiana Tech | 61 | ||||
| Marshall | 14 | at | Southern Miss | 24 | ||||
| North Texas | 17 | at | Texas-San Antonio | 31 | ||||
| Old Dominion | 31 | at | UTEP | 21 | ||||
| 11/5/2016 | Texas-San Antonio | 45 | at | Middle Tenn State | 25 | |||
| Louisiana Tech | 45 | at | North Texas | 24 | ||||
| Marshall | 14 | at | Old Dominion | 38 | ||||
| Florida Atlantic | 42 | at | Rice | 25 | ||||
| UNC-Charlotte | 38 | at | Southern Miss | 27 | ||||
| Houston Baptist | 10 | at | UTEP | 42 | SLC (1AA) | |||
| Florida Intl | 21 | at | Western Kentucky | 49 | ||||
| 11/12/2016 | UTEP | 31 | at | Florida Atlantic | 35 | |||
| Texas-San Antonio | 35 | at | Louisiana Tech | 63 | ||||
| Middle Tenn State | 17 | at | Marshall | 42 | ||||
| Southern Miss | 35 | at | Old Dominion | 51 | ||||
| Rice | 22 | at | UNC-Charlotte | 21 | ||||
| North Texas | 7 | at | Western Kentucky | 45 | ||||
| 11/19/2016 | Old Dominion | 42 | at | Florida Atlantic | 24 | |||
| Marshall | 14 | at | Florida Intl | 31 | ||||
| Southern Miss | 23 | at | North Texas | 29 | ||||
| UTEP | 24 | at | Rice | 44 | ||||
| Texas-San Antonio | 10 | at | Texas A&M | 23 | @ SEC | |||
| Middle Tenn State | 38 | at | UNC-Charlotte | 31 | ||||
| 11/25/2016 | Louisiana Tech | 24 | at | Southern Miss | 39 | |||
| 11/26/2016 | Western Kentucky | 60 | at | Marshall | 6 | |||
| Florida Atlantic | 56 | at | Middle Tenn State | 77 | ||||
| Florida Intl | 28 | at | Old Dominion | 42 | ||||
| Rice | 17 | at | Stanford | 41 | @ P12 | |||
| UNC-Charlotte | 14 | at | Texas-San Antonio | 33 | ||||
| North Texas | 24 | at | UTEP | 52 | ||||
| 12/3/2016 | Louisiana Tech | 44 | at | Western Kentucky | 58 | |||
| 12/17/2016 | Southern Miss | 28 | vs | UL Lafayette | 21 | New Orleans Bowl | vs SBC | |
| New Mexico | 23 | vs | Texas-San Antonio | 20 | Gildan New Mexico Bowl (Albuquerque NM) | vs MW | ||
| 12/20/2016 | Memphis | 31 | vs | Western Kentucky | 51 | Boca Raton Bowl | vs AAC | |
| 12/23/2016 | Louisiana Tech | 48 | vs | Navy | 45 | Armed Forces Bowl (Fort Worth TX) | vs AAC | |
| Eastern Michigan | 20 | vs | Old Dominion | 24 | Popeyes Bahama Bowl (Nassau) | vs MAC | ||
| 12/24/2016 | Hawaii | 52 | vs | Middle Tenn State | 35 | Hawai'I Bowl (Honolulu HI) | vs MW | |
| 12/27/2016 | Army | 38 | vs | North Texas | 31 | OT | Heart of Dallas Bowl | vs Ind |