Through games of Sept. 24, 2016:
| # | School (1st votes) | Rec | Pts | Prev. |
| 1 | Mount Union (19) | 3-0 | 614 | 1 |
| 2 | UW-Whitewater (2) | 3-0 | 588 | 2 |
| 3 | Mary Hardin-Baylor (3) | 3-0 | 579 | 3 |
| 4 | St. Thomas (1) | 4-0 | 565 | 4 |
| 5 | UW-Oshkosh | 3-0 | 522 | 5 |
| 6 | North Central (Ill.) | 4-0 | 467 | 7 |
| 7 | Linfield | 1-1 | 433 | 9 |
| 8 | UW-Platteville | 3-0 | 425 | 10 |
| 9 | Johns Hopkins | 4-0 | 409 | 11 |
| 10 | St. John's | 3-1 | 401 | 6 |
| 11 | Wheaton (Ill.) | 4-0 | 386 | 8 |
| 12 | Hardin-Simmons | 3-0 | 380 | 12 |
| 13 | Salisbury | 3-0 | 309 | 15 |
| 14 | St. John Fisher | 4-0 | 242 | 16 |
| 15 | Huntingdon | 3-0 | 234 | 17 |
| 16 | Thomas More | 3-1 | 197 | 18 |
| 17 | East Texas Baptist | 3-0 | 187 | 19 |
| 18 | Wittenberg | 3-0 | 156 | -- |
| 19 | Franklin | 3-1 | 149 | 20 |
| 20 | Stevenson | 4-0 | 130 | 21 |
| 21 | Hobart | 4-0 | 112 | 22 |
| 22 | Christopher Newport | 4-0 | 91 | 24 |
| 23 | Wabash | 2-1 | 77 | 13 |
| 24 | Central | 4-0 | 58 | 25 |
| 25 | St. Lawrence | 4-0 | 52 | -- |
Dropped out: No. 14 Delaware Valley; No. 23 Cortland.
Others receiving votes: Delaware Valley 49; Hendrix 46; DePauw 32; Alfred 31; John Carroll 31; Claremont-Mudd-Scripps 29; Guilford 23; Utica 21; Whitworth 19; Westminster (Pa.) 15; Case Western Reserve 13; UW-Stevens Point 12; Monmouth 12; Wartburg 7; Dubuque 7; Amherst 6; Wesley 5; Centre 2; Berry 1; Framingham State 1.
The D3football.com Top 25 is voted on by a panel of 25 coaches, Sports Information Directors and media members from across the country, and is published weekly.