He did however score 2 goals in two friendly games at the start of the season.. On 17 July 2008, Linfield gave Thompson permission to negotiate terms with Stockport County after agreeing a fee for the striker believed to be in the region of £100,000 plus add-ons.
Fans bade Thompson an emotional farewell in a flood of messages published on the Linfield website,[4][5][6][7] in which the club branded him one of their greatest players and an exemplary sportsman.
[8] He officially signed for the Cheshire club the following day and was handed the number nine shirt, worn previously by Stockport strikers Kevin Francis, Brett Angell and Luke Beckett.
Thompson was dubbed "A Player To Watch" in League One by the leading newspapers in the UK and bagged his first competitive Stockport goal in their 2–2 draw at Cheltenham on 27 September 2008.
He was forced out of the first team by loan signings better suited to Stockport's tactics, and was hit with a further setback when a chest infection turned serious causing Thompson a collapsed lung.