Most of the university's athletic teams compete at the NCAA Division II level in the Northern Sun Intercollegiate Conference (NSIC).

The men's sports teams include baseball, basketball, cross country, football, golf, ice hockey, track and field and wrestling.

The women's teams include basketball, cross country, golf, ice hockey, soccer, softball, swimming and diving, tennis, track and field, and volleyball.

[9] The men's baseball team has had considerable success in recent years, reaching the College World Series in 2010, 2012, 2013, and 2014.

The Minnesota State football team plays in NCAA Division II and is a member of the Northern Sun Intercollegiate Conference.

Minnesota State alumni who have gone on to the NFL include wide receiver Adam Thielen, offensive lineman Chris Reed, and tight end Bob Bruer.

The Mavericks notably lost in the finals of the 1947 NAIA Division I men's basketball tournament to Marshall University by a score of 73 to 59.

[12] The women's basketball team won the 2009 NCAA Division II national championship with a 103–94 win over Franklin Pierce University on March 27, 2009, in San Antonio, Texas.

The hockey program is currently led by head coach Luke Strand, who replaced Mike Hastings in 2023.

Mavericks alumni who have played in the NHL include Ryan Carter (Anaheim/Carolina/Minnesota), Steve Wagner (St. Louis/Pittsburgh), David Backes (St. Louis), Tim Jackman (Columbus/Phoenix/Los Angeles/New York Islanders/Calgary), Grant Stevenson (San Jose) and Jon Kalinski (Philadelphia).

Under Meyer Minnesota State has won one DII national championship (2017), three North Central Conference titles (1987, 1989, 2007) and four Northern Sun Intercollegiate Conference titles (2012, 2013, 2014, 2016), made 13 trips to the NCAA Division II National Tournament (1987, 1989, 1995, 1997, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2016) and a pair of trips to the NCAA Championships (1987 and 2011).