The 2016 Youngstown State Penguins football team represented Youngstown State University in the 2016 NCAA Division I FCS football season.

They were led by second-year head coach Bo Pelini and played their home games at Stambaugh Stadium.

They were a member of the Missouri Valley Football Conference.

Youngstown State finished the season 12–4 overall with a 6–2 mark in MVFC play to finish in third place.

They received an at-large bid to the FCS playoffs, where they defeated Samford, Jacksonville State, Wofford, and Eastern Washington to advance to the National Championship Game, where they lost to James Madison.