Under Stephen Frail towards the end of the 2007–08 season Thomson played the final five games of the season. This meant upon Csaba László's arrival he was a part of the first team squad. He went on to start the season at right back in Robbie Neilson's absence and played a squad part for much of the season covering when either Neilson or Lee Wallace were out. He signed a new three-year deal in April 2009. Thomson returned to the first team with a start against local rivals Hibs on 7 November 2009, replacing Craig Thomson in the starting line up and was voted the match sponsors man of the match in a very impressive display.