In the 2005–06 season Thomson made his comeback from his injury, establishing himself as one of Hibernian's most important players. He signed a long term contract (until 2010) in March 2006. Thomson was appointed as club captain by Tony Mowbray after the previous captain Gary Caldwell left the club to join Celtic. Despite signing a long term contract with Hibernian, it was still speculated that Thomson would soon leave Hibs. On 31 August 2006, Premier League club Bolton Wanderers made an offer that was rejected by Hibernian.