For 2006, Thompson joined Jason Plato at SEAT Sport UK. He did this at the same time as competing in the WTCC, meaning he had to skip some BTCC rounds when they clashed with World touring car eC in the second SEAT Sport UK car, but at Silverstone for the final round he used his Red Bull-backed WTCC car. After competing in the first nine races, he was actually ahead of BTCC team leader Plato. Despite having to yield the victory to Plato at Croft, he finished sixth overall, scoring more points per entry than any other SEAT driver; although Plato failed to start two races due to accident damage.