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 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
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.
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.)
LSU has won 4 national championships, 1908,1958,2003, and 2007. They were the first college to win 2 BCS National Championships.
UCLA in Men's Division One