In early January 2006, it emerged that Wolverhampton Wanderers manager Glenn Hoddle had shown interest in Wilson during the summer and Heart of Midlothian had made an “active enquiry”, with Celtic and Leeds United also showing an interest in the player who had a £500,000 release clause inserted in his new contract. By the middle of the month, Celtic were rumoured to be close to completing the signing of Wilson and on 16 January, Wilson signed for the club his family had “supported all their life”. Signing for £500,000, Wilson received 25% of the fee under the terms of his contract. He made his debut two weeks later, ironically against Dundee United, playing at right-back in the 3–3 home draw. Wilson suffered a number of injuries in his first full season at Celtic, a broken foot, knee injury and subsequent knee operation.
Wilson became more of a regular in the Celtic side under the management of Neil Lennon. On 1 February 2011, he scored his first goal for Celtic in a 3-0 victory against Aberdeen at Pittodrie Stadium. He got his second goal just 12 days later when he put Celtic 2-0 ahead against his former club Dundee United at Tannadice. On 2 March 2011 during the Scottish Cup fifth round replay against Rangers at Celtic Park, Wilson scored the only goal in what would turn out to be an ill-tempered Old Firm with Rangers receiving three red cards.
It was reported on 30 January 2012 that Wilson was in talks with Leeds United over a potential loan for the remainder of the 2011–12 season, but no deal materialised. On 3 May, Wilson captained Celtic in their 1-0 win against St Johnstone. After the game it was revealed that Wilson would be leaving the club at the end of the season so had been given the captaincy for his last match.