He made his debut with Carlton in Round 10, 2002, against Fremantle after being elevated from the rookie list that year.
The retirements of Stephen Silvagni, Michael Sexton and Ang Christou over a two-year period saw a major gap left in the Carlton defence, and the young Thornton quickly found himself forced to try to fill that hole.
Carlton refused to agree to a trade, stating that Thornton was a required player at the club.
In 2010, the increasing strength of Carlton's backline saw Thornton start to struggle for selection for the first time in his career.
He was picked up by Greater Western Sydney with the first selection in the 2013 Pre-Season Draft, but played only one game for the Giants and was delisted on 4 September 2013.