The 2016 South Dakota Coyotes football team represented the University of South Dakota in the 2016 NCAA Division I FCS football season.

They were led by first-year head coach Bob Nielson and played their home games in the DakotaDome.

They were a member of the Missouri Valley Football Conference.

They finished the season 4–7, 3–5 in MVFC play to finish in a tie for sixth place.