Thomson began his career with Hibernian, before joining Rangers in 2007 for a £2m transfer fee. Thomson won five major trophies with Rangers, including consecutive Scottish Premier League championships in 2009 and 2010. Thomson was also part of the Rangers side which reached the 2008 UEFA Cup Final. Middlesbrough signed Thomson for a fee of £2m in July 2010, but released him in January 2013 after an injury-hit spell. Thomson then rejoined Hibernian in March 2013, but was released in May 2014 after the club was relegated. He then signed for Dundee, before joining Hibernian for a third time.