There were still some residual changes in 1987 due to the folding of the Gulf Star Conference.
1987 FCS Over FBS Victories (17)
- Austin Peay @ Kansas State, 26-22
- Holy Cross @ Army, 34-24
- Western Michigan @ Illinois State, 20-6
- Lamar @ Northern Illinois, 39-35
- William & Mary @ Navy, 27-12
- Youngstown State @ Bowling Green, 20-17
- Lehigh @ Navy, 24-9
- Louisiana Tech @ Kansas, 16-11
- Marshall @ Louisville, 34-31
- Colgate @ Army, 22-20
- Delaware State @ Akron, 52-26
- East Tennessee State @ North Carolina State, 29-14
- Cincinnati @ Indiana State, 40-16
- Louisiana-Monroe @ Southern Miss, 34-24
- Northern Arizona @ Tulsa, 24-20
- Ball State @ Indiana State, 24-23
- Youngstown State @ Akron, 10-6
There was one tie between I-A and I-AA teams in 1987
- Arkansas State @ Memphis, 21-21
Northeast Louisiana (now called Louisiana-Monroe; 13-2 Overall, 6-0 Southland Conference) won their first and only title in a thrilling back-and-forth game against Marshall (10-5 Overall, 4-2 Southern Conference) 43-42.
The Gulf Star Conference was short-lived as it disbanded with the teams moving to the Southland Conference or to I-AA independent status.
Northwestern State, Sam Houston State, Southwest Texas State (now Texas State), and Stephen F. Austin all moved from the folded Gulf Star Conference to the Southland Conference. Nicholls also left but decided to become I-AA independent.
Three Southland teams – Arkansas State, Lamar, and Louisiana Tech – left the conference and became I-AA independents. Towson also joined I-AA status from Division II.
Three teams left their conferences after the 1986 season. Davidson moved from the Southern Conference to the Colonial League (now Patriot League) while Eastern Washington moved from I-AA independent status into the Big Sky. Akron left the Ohio Valley Conference to become an I-AA independent.
The 1987 I-AA Playoffs featured 16 teams with the top four teams seeded. They also used campus sites for the first round, quarterfinals, and semifinals. The national championship was played on December 19 in the Minidome in Pocatello, Idaho.
Two storylines occurred before the playoffs. Holy Cross player Gordie Lockbaum finished third in the Heisman for 1987 but was prevented from playing in the playoffs due to the rules of the Colonial League.
The second was Howard, winners of the MEAC, who sued the NCAA claiming they intentionally not selected for the playoffs. Their claim to halt or include them in the playoffs was denied while the NCAA said Howard had a “weak schedule” thus why they were not included in the field.
The NCAA may have actually made the right decision in the end: Howard was stripped of their 1987 MEAC Championship for fielding at least three ineligible players.