| 9/3/2016 | Bluefield | 7 | at | Campbell | 59 | MSC (NAIA) | ||
| Central State | 19 | at | Dayton | 31 | SIAC (D2) | |||
| Quincy | 38 | at | Drake | 35 | GLV (D2) | |||
| Davidson | 14 | at | Georgetown | 38 | @ Pat | |||
| Valparaiso | 13 | at | Illinois State | 50 | @ MVC | |||
| Butler | 25 | at | Indiana State | 41 | @ MVC | |||
| Morehead State | 7 | at | James Madison | 80 | @ CAAF | |||
| Bucknell | 26 | at | Marist | 10 | Pat | |||
| Western New Mexico | 0 | at | San Diego | 27 | RMAC (D2) | |||
| Sacred Heart | 18 | at | Stetson | 14 | NE | |||
| 9/10/2016 | Franklin | 14 | at | Butler | 59 | HCA (D3) | ||
| San Diego | 16 | at | Cal Poly | 38 | @ BSky | |||
| Campbell | 47 | at | Chowan | 14 | @ CIAA (D2) | |||
| Robert Morris | 0 | at | Dayton | 13 | NE | |||
| Davidson | 35 | at | Kentucky Wesleyan | 21 | @ D2Ind (D2) | |||
| Jacksonville | 7 | at | Liberty | 55 | @ BigS | |||
| Georgetown | 20 | at | Marist | 17 | Pat | |||
| VMI | 17 | at | Morehead State | 13 | SoCon | |||
| Valparaiso | 14 | at | Sacred Heart | 42 | @ NE | |||
| Drake | 28 | at | South Dakota State | 56 | @ MVC | |||
| Warner U. | 15 | at | Stetson | 30 | Sun (NAIA) | |||
| 9/17/2016 | Presbyterian | 31 | at | Campbell | 14 | BigS | ||
| Livingstone | 12 | at | Davidson | 38 | CIAA (D2) | |||
| McKendree | 16 | at | Drake | 28 | GLV (D2) | |||
| Dayton | 20 | at | Duquesne | 34 | @ NE | |||
| Edward Waters | 7 | at | Jacksonville | 41 | Sun (NAIA) | |||
| Lincoln PA | 6 | at | Morehead State | 56 | CIAA (D2) | |||
| Marist | 6 | at | Sacred Heart | 31 | @ NE | |||
| Butler | 27 | at | Taylor | 14 | @ MSFA (NAIA) | |||
| Trinity International | 24 | at | Valparaiso | 49 | MSFA (NAIA) | |||
| 9/24/2016 | Butler | 27 | at | Campbell | 33 | |||
| Morehead State | 28 | at | Drake | 30 | ||||
| Dayton | 22 | at | San Diego | 34 | ||||
| Jacksonville | 24 | at | Stetson | 7 | ||||
| Davidson | 20 | at | Valparaiso | 24 | ||||
| 10/1/2016 | San Diego | 44 | at | Butler | 10 | |||
| Stetson | 31 | at | Davidson | 27 | ||||
| Drake | 10 | at | Dayton | 35 | ||||
| Duquesne | 54 | at | Jacksonville | 35 | NE | |||
| Campbell | 7 | at | Marist | 24 | ||||
| Valparaiso | 26 | at | Morehead State | 29 | ||||
| 10/8/2016 | Stetson | 31 | at | Brown | 21 | @ Ivy | ||
| Marist | 30 | at | Butler | 21 | ||||
| Morehead State | 27 | at | Dayton | 51 | ||||
| Campbell | vs | Jacksonville | Cancelled WX | |||||
| Davidson | 3 | at | San Diego | 52 | ||||
| Drake | 35 | at | Valparaiso | 21 | ||||
| 10/15/2016 | Butler | 20 | at | Davidson | 17 | |||
| San Diego | 38 | at | Drake | 7 | ||||
| Dayton | 36 | at | Jacksonville | 16 | ||||
| Marist | 44 | at | Morehead State | 41 | OT | |||
| Valparaiso | 21 | at | Stetson | 18 | ||||
| 10/22/2016 | Dayton | 31 | at | Butler | 16 | |||
| Stetson | 30 | at | Campbell | 24 | OT | |||
| Davidson | 10 | at | Marist | 31 | ||||
| Jacksonville | 61 | at | Morehead State | 49 | ||||
| Valparaiso | 10 | at | San Diego | 49 | ||||
| 10/29/2016 | Jacksonville | 35 | at | Davidson | 17 | |||
| Stetson | 10 | at | Dayton | 21 | ||||
| Campbell | 21 | at | Drake | 33 | ||||
| San Diego | 27 | at | Marist | 3 | ||||
| Butler | 23 | at | Valparaiso | 12 | ||||
| 11/5/2016 | Morehead State | 54 | at | Butler | 28 | |||
| Davidson | 0 | at | Campbell | 28 | ||||
| Valparaiso | 21 | at | Dayton | 37 | ||||
| Drake | 31 | at | Jacksonville | 27 | ||||
| Marist | 45 | at | Stetson | 38 | ||||
| 11/12/2016 | Butler | 14 | at | Drake | 28 | |||
| Dayton | 59 | at | Marist | 31 | ||||
| Campbell | 27 | at | Morehead State | 21 | ||||
| Stetson | 7 | at | San Diego | 42 | ||||
| Jacksonville | 39 | at | Valparaiso | 42 | ||||
| 11/19/2016 | San Diego | 57 | at | Campbell | 21 | |||
| Morehead State | 31 | at | Davidson | 10 | ||||
| Marist | 35 | at | Jacksonville | 41 | ||||
| Drake | 45 | at | Stetson | 17 | ||||
| 11/26/2016 | San Diego | 35 | at | Cal Poly | 21 | @ BSky | ||
| 12/3/2016 | San Diego | 7 | at | North Dakota State | 45 | 1AA Playoffs | @ MVC |