The Cumbrian finished in second place, just a shot behind eventual winner James Glenn from Durham, after 36 holes at Woodhall Spa Golf Club in Lincolnshire.
Carlisle Golf Club player Thompson, the reigning county strokeplay champion, took on fellow leading county players from across the country at the men’s champion of champions event.
He set an impressive pace with an opening round of 68 to claim a two-shot lead over the field at the halfway stage.
Thompson was the only player to break 70 over the first 18 holes, his excellent five-under-par round on Woodhall Spa’s Hotchkin Course including six birdies.
His second round score of 74, though, enabled Glenn to fight back, the Durham champion adding a 71 to his opening 70.
Durham’s James Glenn pipped Carlisle’s Rory Thompson by a shot(Image: Leaderboard Photography / England Golf)
That saw Glenn post an aggregate score of 141, his five-under total just pipping four-under Thompson.
The Carlisle player came ahead of a host of other contenders, including champions from Staffordshire, Hertfordshire, Somerset, Devon, Lincolnshire, Kent and many more, amid testing conditions on the Lincolnshire course.
Thompson is the latest Cumbrian to perform well on the national county stage.
Recently teenager Rebecca Wildey finished runner-up by a shot in the English girls’ champion of champion event, which was played on Woodhall Spa’s Bracken Course earlier this month.