MacPherson's record at Syracuse was 66–46–4 and included an undefeated season in 1987, when his team finished 11–0–1 and tied Auburn in the 1988 Sugar Bowl. After the 1990 season he left Syracuse to become head coach of the New England Patriots and was replaced by assistant Paul Pasqualoni. MacPherson coached the Pats from 1991 to 1992 and received strong consideration for Coach of the Year honors turning around a team that went 1–15 in 1990 and leading them to a 6–10 record in his first season.