They compete at the NCAA Division III level and are members of the Minnesota Intercollegiate Athletic Conference (MIAC).

McNally stated while leaving the head coaching job that, "nobody can win at Saint John's."

The current coach is Gary Fasching, who was named to the position on December 28, 2012.

[5] The Johnnies have the second highest win percentage football program in Division III history, boasting a 692–257–24 (.724) record during 2024 season.

The Johnnies have made twenty-nine appearances in the NCAA Division III playoffs, with a combined record of 44–27.