The 2016 Stony Brook Seawolves football team represented Stony Brook University in the 2016 NCAA Division I FCS football season. The Seawolves competed as fourth year members of the Colonial Athletic Association with Chuck Priore as the head coach for his eleventh season. They played their home games at Kenneth P. LaValle Stadium in Stony Brook, New York. They finished the season 5–6, 4–4 in CAA play to finish in a tie for sixth place.