The 2016 Florida Atlantic Owls football team represented Florida Atlantic University in the 2016 NCAA Division I FBS football season. The Owls played their home games at the FAU Stadium in Boca Raton, Florida, and competed in the East Division of Conference USA (C–USA). They were led by third-year head coach Charlie Partridge. They finished the season 3–9, 2–6 in C-USA play to finish in a tie for sixth place in the East Division.