Pasqualoni was an assistant at Syracuse from 1987 until 1991, when he was promoted to head coach after the position was vacated by Dick MacPherson, who left for the NFL to coach the New England Patriots. The Orange (then known as the Orangemen) enjoyed a number of successful years with Pasqualoni at the helm. The team won the Fiesta Bowl over Colorado in 1992 and defeated Clemson 41–0 in the Gator Bowl in 1995, Donovan McNabb's freshman year. The team had a 6–3 record in bowl games under Pasqualoni. Pasqualoni's 14-year record with Syracuse was 107–59–1. His only losing season was in 2002 with a 4–8 record. Most seasons of his tenure saw Syracuse competing in the Top 25 in the country.