The 2016 Bethune–Cookman Wildcats football team represented Bethune–Cookman University in the 2016 NCAA Division I FCS football season.

They were led by second-year head coach Terry Sims and played their home games at Municipal Stadium.

They were a member of the Mid-Eastern Athletic Conference (MEAC).

They finished the season 4–6, 4–4 in MEAC play to finish in a two-way tie for fifth place.