Cignetti coached the West Virginia Mountaineers from 1976 to 1979. His record at West Virginia stands at 17–27, but his most success was in NCAA Division II football. He coached Indiana University of Pennsylvania (IUP) to a 182–50–1 record from 1986 to 2005. Under Cignetti, the Indians made their first Division II post-season appearance in 1987. His 28 post-season games is a Division II coaching record, while his 15 playoff wins were second-best when he retired in 2005. In 1991, he was the Division II coach of the year. His teams won 10 Lambert Cups, as the best Division II team in the eastern United States.