The Wildcats previously competed in the Kansas Collegiate Athletic Conference (KCAC) from 1902–03 to 1970–71.

Baker competes in 23 intercollegiate varsity sports: Men's sports include baseball, basketball, bowling, cross country, football, golf, soccer, tennis, track & field and wrestling; while women's sports include basketball, bowling, cross country, golf, soccer, softball, tennis, track & field, volleyball and wrestling; and co-ed sports includes cheerleading, dance and eSports.

The official mascot of Baker University Athletic teams is WOWzer the Wildcat.

WOWZer debuted, as the new mascot, on September 8, 2007, at the football home-opener in honor of the university's sesquicentennial.

Reina Murphy, a freshman from the Kansas City metropolitan area, won the university's name the Wildcat contest.