The Warhawks often rank among the top of NCAA Division III schools in the NACDA Director's Cup standings.

On May 27, 2014, UW–Whitewater made history as the first NCAA institution in any division to win national championships in football, men's basketball, and baseball in a single academic year.

In the 2005 and 2006 seasons, they finished the year undefeated in regular season play, losing only in the Amos Alonzo Stagg Bowls of 2005 and 2006 to the University of Mount Union (then Mount Union College), under former coach and UW–Whitewater alum Bob Berezowitz (UW–Whitewater 1967), who had quarterbacked the UW–Whitewater team as the runner-up in the 1966 National Association of Intercollegiate Athletics playoffs.

The Warhawks ran the table in 2009 with a perfect record of 15–0, defeating Mount Union in the Stagg Bowl 38–28 to claim their second national title in three years.

UW–Whitewater, led by junior quarterback Matt Behrendt, would go on to win by a final score of 52–14 and secure their fifth National Championship, and fourth undefeated season, under coach Leipold.