He joined Martin O'Neill's Wycombe Wanderers in February 1992 for a fee of £15,000 and was part of the Conference and FA Trophy double-winning side.
Together with Kevan Brown, Thompson joined Yeovil Town in March 1998 for a combined fee of £7,500,[1] playing in the side while also acting as the club's fitness coach and working part-time in the postal service.
When Yeovil manager Colin Lippiatt resigned at the end of September 1999, Thompson took over, initially as caretaker, but was awarded the job permanently on 10 November 1999.
On 20 September 2017, Thompson was hired as the new first-team manager of Southern League Premier Division side Dorchester Town.
[7] He was sacked by Dorchester Town Fc on 5 March 2019 due to poor run form and the club relegated to a lower zone than what they were previous to his joining; fans called for his removal.