Wisconsin–La Crosse competes at the NCAA Division III level and is a member of the Wisconsin Intercollegiate Athletic Conference (WIAC).

[7] [8] † Co-champions ‡ The official record book does not reflect the game against the University of Wisconsin–Superior Yellowjackets scheduled for week 4 in 1992.

After completing their non-conference schedule, Wisconsin–Superior suspended its season prior to conference play, before eventually dropping the football program altogether.

In the playoff era, the Eagles finished the regular season undefeated three times (1992, 1993, 1995), winning the National Championship in 1992 and 1995, and losing in the quarterfinals in 1993.

From 1988 to 1999 the university hosted the New Orleans Saints of the National Football League for their preseason training camp.

[15] The Saints chose to use La Crosse to escape the extreme heat and humidity of Louisiana summers, as well as the great football facilities.

[16] Five other NFL teams used campuses across Wisconsin and Minnesota for training camp, in what was known as the Cheese League.