| 9/3/2016 | Wisconsin-River Falls | 20 | at | Coe | 35 | @ IIAC | ||
| Wisconsin-Platteville | 35 | at | George Fox | 0 | @ NWC | |||
| Wisconsin-La Crosse | 45 | at | Luther | 14 | @ IIAC | |||
| Wisconsin-Stevens Point | 37 | at | St Norbert | 14 | @ MidW | |||
| St Thomas | 42 | at | Wisconsin-Eau Claire | 6 | MIA | |||
| John Carroll | 14 | at | Wisconsin-Oshkosh | 33 | OAC | |||
| Simpson | 30 | at | Wisconsin-Stout | 45 | IIAC | |||
| New Jersey | 3 | at | Wisconsin-Whitewater | 51 | NJAC | |||
| 9/10/2016 | Wisconsin-Eau Claire | 7 | at | Concordia-Moorhead | 25 | @ MIA | ||
| Wisconsin-River Falls | 21 | at | Gustavus Adolphus | 24 | @ MIA | |||
| Wisconsin-Stout | 17 | at | St Thomas | 57 | @ MIA | |||
| Ripon | 14 | at | Wisconsin-La Crosse | 65 | MidW | |||
| St Francis IL | 7 | at | Wisconsin-Platteville | 26 | MSFA (NAIA) | |||
| Albion | 13 | at | Wisconsin-Stevens Point | 50 | MIAA | |||
| Belhaven | 13 | at | Wisconsin-Whitewater | 59 | ASWC | |||
| 9/17/2016 | Wisconsin-Oshkosh | 68 | at | Finlandia | 7 | @ D3Ind | ||
| Wisconsin-Stout | 23 | at | Mayville State | 13 | @ NSAA (NAIA) | |||
| 9/24/2016 | Wisconsin-Stevens Point | 44 | at | Adrian | 19 | @ MIAA | ||
| Wisconsin-La Crosse | 41 | at | Carroll WI | 7 | @ MidW | |||
| Wisconsin-Platteville | 56 | at | Lakeland | 0 | @ NAC | |||
| Southwestern Texas | 22 | at | Wisconsin-River Falls | 42 | SCAC | |||
| Morningside | 21 | at | Wisconsin-Whitewater | 35 | GPAC (NAIA) | |||
| Wisconsin-Eau Claire | 40 | at | Wisconsin Lutheran | 14 | @ NAC | |||
| 10/1/2016 | Wisconsin-Stevens Point | 28 | at | Wisconsin-Eau Claire | 19 | |||
| Wisconsin-River Falls | 14 | at | Wisconsin-La Crosse | 35 | ||||
| Wisconsin-Stout | 17 | at | Wisconsin-Oshkosh | 45 | ||||
| Wisconsin-Whitewater | 30 | at | Wisconsin-Platteville | 24 | ||||
| 10/8/2016 | Wisconsin-Eau Claire | 21 | at | Wisconsin-River Falls | 41 | |||
| Wisconsin-Platteville | 47 | at | Wisconsin-Stevens Point | 31 | ||||
| Wisconsin-La Crosse | 42 | at | Wisconsin-Stout | 6 | ||||
| Wisconsin-Oshkosh | 14 | at | Wisconsin-Whitewater | 17 | ||||
| 10/15/2016 | Wisconsin-Whitewater | 32 | at | Wisconsin-La Crosse | 22 | |||
| Wisconsin-River Falls | 14 | at | Wisconsin-Platteville | 45 | ||||
| Wisconsin-Oshkosh | 13 | at | Wisconsin-Stevens Point | 3 | ||||
| Wisconsin-Eau Claire | 7 | at | Wisconsin-Stout | 30 | ||||
| 10/22/2016 | Wisconsin-La Crosse | 14 | at | Wisconsin-Eau Claire | 20 | |||
| Wisconsin-Platteville | 13 | at | Wisconsin-Oshkosh | 22 | ||||
| Wisconsin-Stout | 28 | at | Wisconsin-River Falls | 50 | ||||
| Wisconsin-Stevens Point | 2 | at | Wisconsin-Whitewater | 24 | ||||
| 10/29/2016 | Wisconsin-Whitewater | 48 | at | Wisconsin-Eau Claire | 6 | |||
| Wisconsin-Stevens Point | 38 | at | Wisconsin-La Crosse | 22 | ||||
| Wisconsin-Oshkosh | 41 | at | Wisconsin-River Falls | 7 | ||||
| Wisconsin-Platteville | 55 | at | Wisconsin-Stout | 27 | ||||
| 11/5/2016 | Wisconsin-La Crosse | 29 | at | Wisconsin-Oshkosh | 51 | |||
| Wisconsin-Eau Claire | 0 | at | Wisconsin-Platteville | 56 | ||||
| Wisconsin-Stout | 28 | at | Wisconsin-Stevens Point | 35 | ||||
| Wisconsin-River Falls | 20 | at | Wisconsin-Whitewater | 27 | OT | |||
| 11/12/2016 | Wisconsin-Oshkosh | 48 | at | Wisconsin-Eau Claire | 13 | |||
| Wisconsin-Platteville | 63 | at | Wisconsin-La Crosse | 45 | ||||
| Wisconsin-Stevens Point | 16 | at | Wisconsin-River Falls | 34 | ||||
| Wisconsin-Whitewater | 34 | at | Wisconsin-Stout | 16 | ||||
| 11/19/2016 | Wisconsin-Platteville | 31 | at | St John's MN | 32 | @ MIA | ||
| Washington U | 13 | at | Wisconsin-Oshkosh | 49 | SAA | |||
| Lakeland | 27 | at | Wisconsin-Whitewater | 45 | NAC | |||
| 11/26/2016 | St John's MN | 14 | at | Wisconsin-Oshkosh | 31 | MIA | ||
| Wittenberg | 9 | at | Wisconsin-Whitewater | 37 | NCA | |||
| 12/3/2016 | Wisconsin-Oshkosh | 34 | at | St Thomas | 31 | D3 Quarterfinal | @ MIA | |
| John Carroll | 31 | at | Wisconsin-Whitewater | 14 | D3 Quarterfinal | OAC | ||
| 12/10/2016 | John Carroll | 3 | at | Wisconsin-Oshkosh | 10 | D3 Semifinal | OAC | |
| 12/16/2016 | Mary Hardin-Baylor | 10 | vs | Wisconsin-Oshkosh | 7 | D3 Championship (Salem VA) | vs ASWC |