| 8/27/2016 | Grand View (9-3,9-2) | 13 | at | Baker | 36 | | | |
| 9/3/2016 | Culver-Stockton (1-10,1-10) | 27 | at | Baker | 89 | | | |
| 9/10/2016 | Baker | 41 | at | William Penn (7-4,7-4) | 7 | | | |
| 9/17/2016 | Baker | 44 | at | Graceland (5-6,5-6) | 15 | | | |
| 9/24/2016 | Benedictine KS (7-4,7-4) | 7 | at | Baker | 60 | | | |
| 10/1/2016 | Baker | 42 | at | Peru State (5-6,5-6) | 21 | | | |
| 10/15/2016 | Avila (0-11,0-11) | 7 | at | Baker | 52 | | | |
| 10/22/2016 | Baker | 55 | at | MidAmerica Nazarene (6-5,6-5) | 34 | | | |
| 10/29/2016 | Baker | 73 | at | Central Methodist (2-9,2-9) | 26 | | | |
| 11/5/2016 | Missouri Valley (9-3,9-2) | 28 | at | Baker | 31 | | | |
| 11/12/2016 | Evangel (4-7,4-7) | 13 | at | Baker | 46 | | | |
| 11/19/2016 | Sterling (8-3) | 21 | at | Baker | 44 | | | KCAC |
| 11/26/2016 | Lindsey Wilson (11-2) | 27 | at | Baker | 42 | | | MSC |
| 12/3/2016 | Eastern Oregon (10-3) | 41 | at | Baker | 45 | | NAIA Semifinal | Front |
| 12/17/2016 | St Francis IN (13-1) | 38 | vs | Baker | 17 | | NAIA Championship (Daytona Beach FL) | MSFA |