While attending Millersville University, Scott was a four-year letterman, and a four-time All-PSAC selection. He finished his career as the school's all-time leader in receptions (240), receiving yards (3,293), touchdowns (27).
While on the Philadelphia Eagles roster, Scott made the game winning catch from A.J. Feeley against the New York Jets in the preseason finale, earning him Player of the Game honors. Scott did not make the 53-man roster, but spent the rest of the 2001 season on the practice squad. Scott resigned with the Eagles and participated in the 2002 and 2003 Eagles training camps before making his debut in the Arena Football League in 2004 for the Philadelphia Soul. In 2006, while on the Philadelphia Soul, Sean Scott came up 1 yard short of 1,000 yards receiving, and led in his team in Receiving Yards that season.