Born in, Shropshire, Thompson began his career as a youth player with hometown club Shrewsbury Town.

He made his senior début as a 19-year-old under manager Jake King, in a 3–0 away win over Torquay United on the last day of the 1998–99 Division Three season.

Shortly after his arrival at Edgar Street, he picked up an injury and so missed out on the opportunity to play when first choice goalkeeper Wayne Brown was injured in the first league game.

When he recovered from his injury, loanee Scott Tynan was preferred as first choice goalkeeper until the return of Brown.

This came in the Football League Trophy against his former club Shrewsbury, and he also appeared for the reserves and in the HFA Senior Cup.