The 1999 Youngstown State Penguins football team was an American football team represented Youngstown State University in the Gateway Conference during the 1999 NCAA Division I-AA football season. In their 14th season under head coach Jim Tressel, the team compiled a 12–3 record (5–1 against conference opponents) and lost to Georgia Southern in the 1999 NCAA Division I-AA Football Championship Game. It was Youngstown State's sixth appearance in the national championship game during the 1990s.