On April 28, 2009 the university board of trustees voted to leave the NAIA and apply to join the NCAA Division II. For two years, USF remained a member of the NAIA and Great Plains Athletic Conference. In 2011–2012, the school became a provisional member of the NCAA, playing full NCAA schedules and required to operate under NCAA Division II regulations but was ineligible for postseason events. In July 2012, the university became one of six universities to join the NCAA as full members, with official membership commencing on September 1, 2012. As part of the successful transition to the NCAA, the Cougars will be eligible for postseason conference and NCAA postseason competition. With the acceptance into the NCAA as a full member, the university will begin conference play in the NSIC for the majority of sports and in the GNAC for men's soccer.
Sports
The USF Athletic Department sponsors the following sports: Men's intercollegiate athletic teams
Wrestling,and men's tennis were dropped once USF moved to NCAA Division II in 2011. In The Spring of 2013 USF Dropped Men's Soccer after one year in DII The tennis team had made five trips to the NAIA Championships in 2003, 2004, 2007, 2008, and 2010.
Football
The University of Sioux Falls Cougars football team, which is led by third year coach Jon Anderson, won the NAIA Division II Football National Championship in 1996, and the NAIA Football National Championship in 2006, 2008 and 2009. All four of USF's national championships have been undefeated seasons. The football program has had four NAIA Players of the Year Award winners, running back Nick Kortan in 2002, quarterback Chad Cavender in 2007, quarterback Lorenzo Brown in 2009 and receiver Jon Ryan in 2010. The program has won 19 conference titles, including 10 in the SDIC and 9 in the GPAC. From 2008–2010 the team sported a 42-game winning streak which tied an NAIA record. The current head coach is Jon Anderson who replaced Jed Stugart. Anderson is 24-11 in three seasons at USF. Stugart took over for alum Kalen DeBoer in 2010. DeBoer led USF to a 67-3 record in his five years with 3 national titles as head coach. Legendary coach Bob Young led the Cougars from 1983– 2004 guiding them to their first national championship in 1996.
The USF baseball team, now directed by head coach Grant Hieb, won the 2007 GPAC regular and postseason titles with a record of 17–7. They had a breakout season in the spring of 2010, setting a school record for wins in a season with a 33–17 record. The Cougars finished second in the GPAC with a 19–5 conference record. In 2012, the Cougars moved to NCAA DII and joined the NSIC.
Basketball (men's)
The men's basketball team advanced to 9 NAIA Tournaments, including a Final Four Appearance in 2004. USF won two regular season GPAC Titles and 4 postseason GPAC Titles. The current coach is Chris Johnson, who has led the Cougars to tournament appearances in each of his three seasons, including Sweet Sixteen appearances in 2009 and 2010. He has 200 career wins at USF with 216 in his career with 159 losses. He is 200-144 at USF
Basketball (women's)
The women's basketball team advanced to the NAIA Tournament in 2001, 2003, and 2011. The 2003 team is the only Final Four team in school history. The 2011 team, under current coach Travis Traphagen, reached the Elite 8 and set a school record for wins with 27. He has 224 career wins and all at USF where he has led the Cougars to 20 win seasons in four of the past five years. The Cougars were ranked No. 11 in WBCA poll for their highest ranking at the DII level. USF made an appearance in the NCAA DII Championships after claiming the 2015-16 NSIC Tournament title and earning the automatic berth to the regional.
Golf (women's)
The 2007–2008 women's golf team won the GPAC Championship. Tavia Rutherford is the head coach for both men's and women's programs beginning in 2019.
Softball
The women's softball team, directed by head coach Shannon Pivovar, advanced to the NAIA Softball World Series in 2005. That team also won the only postseason GPAC title in school history and finished with a 29-16 record, a school record for victories.
Tennis (women's)
The women's tennis team, led by head coach Kevin Grebin, made four trips to the NAIA Championships in 2000, 2004, 2005, 2010. They won regular season GPAC titles in 2005, 2009, and 2010 and postseason GPAC titles in 2004, 2005, and 2010.
Track and Field
The track and field team, which is directed by Doug Petersen, has four NAIA individual national champions: Vinnie Olson, Colin Koth, and Brigitte Gross. Since joining the NCAA, the track and field program has added 3 more national champions: Jagger Gran, Scott Greenman, and Courtney Crandall The women's outdoor team won the GPAC title in 2011.
