Thomson joined Hibernian on 10 August 2001. He was one of a group of young players who came through their youth team during the early 2000s, also including Steven Whittaker, Derek Riordan, Scott Brown and Garry O'Connor. Thomson established himself as a regular in the Hibernian first team during the 2003–04 season and played in that season's Scottish League Cup final defeat by Livingston, but he suffered a serious cruciate ligament injury during a game against Partick Thistle near the end of that season. The injury meant that he was out of football for almost a year, and he consequently made only four league appearances in the 2004–05 season.