Thornton began his career with Football League Second Division club Tranmere Rovers in 2001, for whom he made 13 appearances in the 2001–02 season,[3] scoring once against Wigan Athletic.
[10] He made his debut for Sunderland in a FA Cup third-round replay win over Bolton Wanderers in January 2003, impressing manager Howard Wilkinson who said, "That was the first full game I've seen Sean in and I must say it was a very promising and mature performance.
[29][30] Manager Dave Penney praised Thornton, saying: "It was a great goal for Sean and he's looking much brighter and sharper these days, and long may that continue.
"[32] In the 2006–07 season, Thornton made 41 appearances,[33] and helped Doncaster to victory over Bristol Rovers in the Football League Trophy final in April 2007 when he swung in a corner kick for Graeme Lee to head in to score the extra time winner at the Millennium Stadium, Cardiff.
[34] Thornton was released by Doncaster manager, Sean O'Driscoll at the end of the 2006–07 season,[35] and joined another League One side, Leyton Orient in July 2007 on a two-year contract.
"[36] He scored on his debut against Southend United in August 2007, with a spectacular free kick from 30 yards in a 2–1 away win,[38] and went on to make 34 appearances in the 2007–08 season,[39] although he missed four matches after being sent off in October 2007 for allegedly punching another player.
[44][45] He signed a new one-year contract with Orient in June 2009, with the option of a further year,[45] but was released by Williams' replacement Russell Slade on 9 May 2010 after putting on too much weight.
The midfielder scored his first goal in Aber colours on 11 November 2011, as the Seasiders hammered Port Talbot Town 4–0 at the Genquip Stadium.
On 16 November 2011, it was announced that Thornton had agreed to extend his stay with Aberystwyth Town until the end of the 2011/12 Welsh Premier League campaign.
Upon seeing his contract out with Drogheda United Thornton was recruited by newly-formed Non League side Rathmullen Celtic who play in Division 3 of the NEFL.
Under the guidance of Chairman Robbie McDonnell and manager Stewie Barnett Thornton masterminded promotion to Div 2 for Rathmullen after reproducing arguably some of the best form of his career.
After one season at Athboy which resulted in a failed promotion attempt, Thornton followed manager Derek Kavanagh to the premier league of the NEFL and to 2017 treble winners Newfoundwell FC.