[2] Prior to joining the NCAA, the Cougars previously competed in the Great Plains Athletic Conference (GPAC) of the National Association of Intercollegiate Athletics (NAIA) from 2000–01 to 2010–11; and in the defunct South Dakota Intercollegiate Conference (SDIC) from 1977–78 to 1999–2000.

On April 28, 2009 the university board of trustees voted to leave the NAIA and apply to join the NCAA Division II.

[2] USF competes in 18 intercollegiate varsity sports: Men's sports include baseball, basketball, cross country, football, golf, track & field, and wrestling; while women's sports include basketball, cheerleading, cross country, golf, soccer, softball, swimming & diving, tennis, track & field, wrestling and volleyball.

Former sports included men's tennis, which was dropped once USF moved to NCAA Division II in 2011 and in the spring of 2013 USF dropped Men's Soccer after one year in DII [7] The tennis team had made five trips to the NAIA Championships in 2003, 2004, 2007, 2008, and 2010.

[12] 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 (26–19 overall).

The 2011 team, under current coach Travis Traphagen, reached the Elite 8 and set a school record for wins with 27.

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.

[16] The women's tennis team, led by head coach Kevin Grebin, made four trips to the NAIA Championships in 2000, 2004, 2005, 2010.