After four years of high school hockey at The Taft School in Watertown, Connecticut, Shannon began college hockey with Boston College in 2001–02. In his freshman year, he received the team's Bernie Burke Award as top rookie after recording 25 points in 38 games. In his senior year, Boston captured the Hockey East championship (The Lamoriello Trophy) and Shannon was named to the Hockey East All-Conference First Team and the All-American East Second Team for the second consecutive season. Scoring 45 points, he earned team MVP honors with two other teammates. Internationally, Shannon represented the U.S. at the 2003 World Junior Championships in his sophomore year.