Walton was hired in 1993 to build the program from scratch. After posting 13 wins as an independent his first two years at the helm, Walton led the Colonials into NEC football in 1996 by winning the first of five consecutive conference championships. During the five-year run, Robert Morris posted a 39-13 overall record and 26-2 mark in league play, and recorded the only undefeated season in school history with a 10–0 mark in the 2000 campaign. The Colonials won back-to-back ECAC Bowls in 1996 and 1997, and were crowned NCAA I-AA non-scholarship national champions in both 1999 and 2000.