The 2016 Saint Francis Cougars football team represented the University of Saint Francis, located in Fort Wayne, Indiana, in the 2016 NAIA football season. They were led by head coach Kevin Donley, who served his 19th year as the head football coach at Saint Francis. The Cougars played their home games at Bishop John D'Arcy Stadium and were members of the Mid-States Football Association (MSFA) Mideast League (MEL). The Cougars finished 2nd in the MSFA MEL division and received an at-large bid to the NAIA playoffs.