Larry Kehres, of Mount Union College, Division III, with 9 national championships.
Division 1 (BCS) Notre Dame 8 championships Division 1 AA (FCS) Georgia Southern 6 championships Division II North Dakota State 5 championships Division III Mount Union 10 championships
The Bulldogs have won two consensus NCAA Division 1-A college football National Championships and 12 Southeastern Conference championships.
In college lacrosse, Johns Hopkins has won 44 national championships -- 35 of these were earned prior to the first NCAA Division I tournament in 1971.
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 10 national championships.(If you meant Division I-FBS, the answer is Paul "Bear" Bryant, no matter how you slice it. So please don't clutter this answer with a bunch of also-rans who came CLOSE to having as many as Bryant. The Bear is the King.)
The NCAA record is 31 consecutive national championships, 1980 to 2010, in Men's Swimming & Diving, Division III, by Kenyon College (Gambier, Ohio). This was the longest streak in any division in any sport in NCAA history.The NCAA record for most total championships in any one sport is the same - Kenyon College - Men's Swimming & Diving - 31 total NCAA national championships.
LSU has won 4 national championships, 1908,1958,2003, and 2007. They were the first college to win 2 BCS National Championships.