Minnesota Morris first joined NCAA Division II Northern Sun Intercollegiate Conference (NSIC) in 1966.

[5] The Minnesota Morris Cougars football team played its first game in the fall of 1961, a 6–3 victory over North Dakota State College of Science under head coach Bruce Rolloff.

Minnesota Morris has played against Bemidji State University 39 times, more than any other team in Cougar history.

Minnesota Morris then experienced a painful decline from 1990 to 2002, after winning just 16 of 130 games, causing them to drop to Division III in 2003.

A 2001 April Fool's issue of The University Register made fun of the losing streak in football by reporting that the recruitment of a multi-talented player named Jesus Christ had put the coach in a bind, "since they have 22 positions that need help.