Dayton has won two national championships, both during their tenure in Division III.
Dayton has made five appearances in the NCAA Division III National Championship Game, also known as the Stagg Bowl. The Flyers defeated Ithaca, 63–0 in the 1980 championship game, and defeated Union (NY) 17–7 in the 1989 championship game. The Flyers were unsuccessful in three other championship game appearances, losing 17–10 to Widener in 1981, 19–3 to Wagner in 1987, and 34–20 to Ithaca in 1991.
From 2001–2005, the Pioneer Football League was divided into North and South Divisions, with the winners of those divisions participating in a Conference Championship Game. As winners of the Pioneer Football League's North Division, Dayton has made two appearance in the Pioneer Football League Championship Game, in 2001 and 2002.