The 2016 Morehead State Eagles football team represented Morehead State University in the 2016 NCAA Division I FCS football season.

They were led by fourth-year head coach Rob Tenyer and played their home games at Jayne Stadium.

[1] They were members of the Pioneer Football League.

They finished the season 4–7, 3–5 in PFL play to finish in a two-way tie for seventh place.