There was quite a bit of movement within conferences and a few programs left I-AA or disbanded their program.
1986 FCS Over FBS Victories (17)
- Louisiana Tech @ Tulsa, 22-17
- Cal State Fullerton @ Nevada, 49-3
- Akron @ Kent State, 17-7
- Arkansas State @ Memphis, 30-10
- Marshall @ Ohio, 21-7
- Northern Iowa @ Kansas State, 17-0
- Cal State Fullerton @ Idaho, 25-17
- Morehead State @ Wichita State, 36-35
- Texas State @ Rice, 31-6
- Western Illinois @ Northern Illinois, 10-0
- Holy Cross @ Army, 17-14
- North Texas @ TCU, 24-20
- Penn @ Navy, 30-26
- William & Mary @ Virginia, 41-37
- Illinois State @ Wichita State, 17-10
- Delaware @ Navy, 27-14
- Louisiana Tech @ Louisiana, 23-14
There were two ties involving I-A and I-AA teams in 1986:
- Furman @ Georgia Tech, 17-17
- Arkansas State @ Mississippi, 10-10
Georgia Southern (13-2 Overall as I-AA Independent) became the first team to win back-to-back titles by crushing Arkansas State (12-2-1 Overall, 5-0 Southland Conference) by a score of 48-21.
The Colonial League (currently known as the Patriot League) was created while the Gateway Conference (now known as the Missouri Valley Football Conference) membership was solely I-AA teams only.
Bucknell, Colgate, Holy Cross, Lafayette, and Lehigh all moved from I-AA independent status to the Colonial League. Both Delaware and Richmond moved from I-AA independent status to the Yankee Conference.
The Gateway Conference was comprised of Eastern Illinois, Illinois State, Indiana State, Missouri State, Northern Iowa, Southern Illinois, and Western Illinois.
A number of teams no longer participated in I-AA football. Drake, Southeastern Louisiana, and Texas-Arlington all dropped their programs after the 1985 season. West Texas A&M dropped from I-AA to Division II.
The I-AA Playoffs expanded from 12 to 16 teams starting with the 1986 season with the top four teams being seeded and the first three rounds played at campus sites. The title game was played on December 19 in the Tacoma Dome in Tacoma, Washington for the second straight season (and last time to date).