2006 Northwestern Football Schedule
- * Conference Event
- %Scrimmage
- ^ Exhibition
- Event times are (CST)
| | Day | Time | Location | | Opponent | Score | | | Record |
| September |
| | 2 | 6:00 PM | | vs. | Dakota State University | W-44-7 | | | 1-0 |
| * | 9 | 7:00 PM | | vs. | Morningside | W-33-7 | | | 2-0 1-0 |
| * | 16 | 7:30 PM | | @ | Doane | W-56-0 | | | 3-0 2-0 |
| * | 23 | 1:00 PM | | vs. | Nebraska Wesleyan | W-36-0 | | | 4-0 3-0 |
| * | 30 | 1:30 PM | | @ | Dakota Wesleyan | W-48-10 | | | 5-0 4-0 |
| October |
| * | 7 | 1:30 PM | | vs. | University of Sioux Falls | L-14-17 | | | 5-1 4-1 |
| * | 14 | 1:00 PM | | @ | Concordia | W-42-27 | | | 6-1 5-1 |
| * | 21 | 1:00 PM | | vs. | Hastings | W-42-13 | | | 7-1 6-1 |
| * | 28 | 1:00 PM | | @ | Briar Cliff | W-41-7 | | | 8-1 7-1 |
| November |
| * | 4 | 1:00 PM | | vs. | Dana College | W-42-10 | | | 9-1 8-1 |
| * | 11 | 1:00 PM | | @ | Midland | W-38-7 | | | 10-1 9-1 |
| | 18 | 12:00 PM | | vs. | Black Hills State University | W-17-10 | | | 11-1 |
| | NAIA Football Championship Series - First Round |
| | 25 | 1:30 PM | | @ | Missouri Valley College | L-26-33 | | | 11-2 |
| | NAIA Football Championship Series - Quarterfinal Round |
