The actor reached the mutual decision with producers of the show after they agreed that his character Jesse Chadwick has "run his course", The Mirror reports.
A source said: "Everyone thinks Jesse has done all he can, so it's time to move on."
Thomson joined the ITV1 drama for a guest stint in September 2008 and appeared on screen towards the end of the year. In January 2009, he signed up to be part of the cast on a permanent basis.
The former Cold Feet star is expected to say farewell to his soap colleagues tonight at a party in Manchester, where the show's stars are planning to celebrate their recent success at the National Television Awards.
Thomson and his wife Sam Sharp are currently expecting their second child together.