Thomson trained with Hibernian, one of his former clubs, in February 2013. A move appeared unlikely because Hibs had no spare budget to pay Thomson with, but he decided in March to forego any salary and signed with the club until the end of the 2012–13 season. Thomson made his second debut appearance for Hibs in a goalless draw against Hearts on 10 March. He agreed a new one-year contract with Hibs in July 2013. Thomson dropped out of the Hibs team after manager Pat Fenlon was replaced with Terry Butcher, and was made available for transfer in January 2014. Thomson was released by Hibs following their relegation to the Scottish Championship.