CiteDiv. 1–A Conference Champs
| Atlantic Coast | Clemson | 6–1 |
| Big Eight | Nebraska | 7–0 |
| Big Ten | Michigan | 7–0–1 |
| Big West | Fresno St. | 7–0 |
| Mid-American | Western Michigan | 7–1 |
| Pac-10 | Southern Cal | 8–0 |
| Southeastern | Auburn/LSU | 6–1 |
| Southwest | Arkansas | 7–0 |
| Western Athletic | Wyoming | 8–0 |
| Bowl Games with Top 20 Teams | 1988 College Football Recap | Heisman Trophy Voting |