Thompson was a youth-team player and came through the academy at Manchester United between 1998-2005 but spent the majority of his senior football career at Rochdale, making over 200 appearances for the club across two permanent spells between 2006-12 and 2016-19, having also played for Tranmere, Carlisle and Bury in addition to loan stints at Wrexham, Southport and another at Rochdale.