The 2016 Saint Francis Red Flash football team represented Saint Francis University in the 2016 NCAA Division I FCS football season.

They were led by seventh-year head coach Chris Villarrial and played their home games at DeGol Field.

They were a member of the Northeast Conference.

[1] They finished the season 7–5, 5–1 in NEC play to finish in a tie for the conference title with Duquesne.

Due to their head-to-head win over Duquesne, they received the NEC's automatic bid to the FCS Playoffs where they lost in the first round to Villanova.