The 1999 NCAA Division II football season, part of college football in the United States organized by the National Collegiate Athletic Association at the Division II level, began on August 28, 1999, and concluded with the NCAA Division II Football Championship on December 11, 1999, at Braly Municipal Stadium in Florence, Alabama, hosted by the University of North Alabama. Northwest Missouri State defeated Carson–Newman in the championship game, 58–52 after four overtimes, to win their second Division II national title.