The 2006 Youngstown State Penguins football team represented Youngstown State University in the 2006 NCAA Division I FCS football season. The team was led by sixth-year head coach Jon Heacock and played their home games at Stambaugh Stadium in Youngstown, Ohio. The Penguins finished the season with an 11–3 record overall and a 6–1 mark in Gateway Football Conference play, making them conference champions. They qualified for the NCAA Division I Football Championship playoffs, where they lost to eventual champion Appalachian State in the semifinals. The team was ranked No. 4 in The Sports Network's postseason NCAA Division I FCS poll.
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