The University of Southern California has the most NCAA national championships in Baseball with 12 wins.
In college football Alabama has the most national championships with 13 while Notre Dame comes in second with 12. In College Hockey Bemidji State University has 13 national championships
Larry Kehres, of Mount Union College, Division III, with 9 national championships.
The University of Michigan has the most with 11 national championships the last in 1997. GO BLUE
Stanford with 540
Alabama. The University of Alabama has 12 National Championships
Depends on which sport or sports you are asking about.