1988 was a quiet season with only four team changes and no conference additions or changes.
1988 FCS Over FBS Victories (11)
- Boise State @ Long Beach State, 29-10
- North Texas @ Texas Tech, 29-24
- Ohio @ Marshall, 31-14
- Idaho @ Pacific, 36-26
- Toledo @ McNeese, 46-19
- Navy @ The Citadel, 42-35
- Louisiana Tech @ Kansas State, 31-28
- Arkansas State @ Akron, 13-12
- Louisiana @ Louisiana Tech, 19-16
- Arkansas State @ Louisiana, 38-21
- North Texas @ Rice, 33-17
There was also one tie between I-A and I-AA teams in 1988:
- Appalachian State @ Wake Forest, 34-34
Furman (13-2 Overall, 6-1 Southern Conference) captured their only I-AA/FCS with a close victory over Georgia Southern (12-3 Overall as I-AA Independent) by a score of 17-12. These two teams also contested the 1985 I-AA Championship with Georgia Southern winning that game.
There were no conference changes in effect for the 1988 season.
Youngstown State left the Ohio Valley Conference to go to I-AA independent status. Conversely, Tennessee State did the opposite: they joined the Ohio Valley from I-AA independent status. Liberty jumped up from Division II to become an I-AA independent. Villanova moved from I-AA independent status to the Yankee Conference.
As with the previous two seasons, the 1988 I-AA Playoffs consisted of 16 teams with the top four seeded. Campus sites were used for the first round, quarterfinals, and semifinals. The title game was held on December 17 in Holt Arena in Pocatello, Idaho for the second straight year (and the final time to date).