The final season of the 1980s saw a recurring theme: change with teams entering and leaving the subdivision.
1989 FCS Over FBS Victories (13)
- Appalachian State @ Wake Forest, 15-10
- Arkansas State @ Memphis, 17-13
- Lamar @ UTEP, 21-19
- Northern Iowa @ Kansas State, 10-8
- The Citadel @ Navy, 14-10
- Akron @ Youngstown State, 20-17
- Akron @ Eastern Illinois, 21-17
- Liberty @ Eastern Michigan, 25-24
- Youngstown State @ Central Michigan, 30-3
- James Madison @ Navy, 24-20
- Morehead State @ Cincinnati, 13-10
- UNLV @ Nevada, 45-7
- Navy @ Delaware, 10-9
There was one tie between I-A and I-AA teams in 1989:
- Akron @ Murray State, 31-31
Georgia Southern (15-0 Overall as I-AA Independent) ended the decade with their 3rd I-AA/FCS title. It was their third national title win and fourth title game appearance in five seasons. They defeated Stephen F. Austin (12-2-1 Overall, 5-0-1 Southland Conference) in a 37-34 contest.
There were no conference changes at the I-AA level in 1989.
Louisiana Tech left I-AA to become I-A independent status while three other teams made the move to I-AA independent status. Davidson left the Colonial (now Patriot League), Fordham moved up from the Division III Liberty Conference, and Samford went from being a Division III independent to the same at the I-AA level.
For the fourth consecutive season, the I-AA Playoff format remained unchanged with a field of 16, the top four teams being seeded, and campus sites used through the semifinal round. The title game was played on December 16 at Paulson Stadium in Statesboro, Georgia for the first time.