Cornell began the season dubbed by sports analysts to have Ivy League championship potential and coach Maxie Baughan described his team as "the sleeping giant of the Ivy League." The Big Red eventually entered the final week of the season, in which they would face their undefeated rivalPenn, having lost two games and tied one; Penn was the last remaining undefeated Division I-AA football team in 1988 and had won or shared the Ivy League title five times in the previous six seasons. During the game, which Cornell would have to win to share the conference title with Penn, nine personal fouls were assessed between the two teams. Cornell eventually broke a 3–3 halftime tie to deliver Penn's first defeat of the season and win a share of the Ivy League title for the first time since 1971.
The 1988 season was Maxie Baughan's sixth and final season as head coach of the Cornell Big Red; he resigned in early 1989 after allegations surfaced that the married Baughan had a romantic relationship with top assistant coach Peter Noyes' wife. Baughan cited "personal tensions" as the rationale for his decision. Assistant coach Jack Fouts was appointed head coach shortly thereafter.