The 2004 Saint Francis Cougars football team represented the University of Saint Francis, located in Fort Wayne, Indiana, in the 2004 NAIA football season. They were led by head coach Kevin Donley, who served his 7th year as the first and only head coach in the history of Saint Francis football. The Cougars played their home games at Bishop John M. D'Arcy Stadium and were members of the Mid-States Football Association (MSFA) Mideast League (MEL). The Cougars finished in 1st place in the MSFA MEL division, and they received an automatic bid to the 2004 postseason NAIA playoffs.