For 2009, rumours had placed Thompson with a possible return to the BTCC after discussions with Team Dynamics to race one of their Honda Civics. He also tested a Tempus Sport Chevrolet Lacetti and a Motorbase Performance BMW 320si. However, his name was missing from the pre-season entry list, and it was later announced he would spend another year in the Danish series. It was then announced in April, prior to the Thruxton round that he would return to the BTCC, replacing Gordon Shedden. He collected a double win at Donington Park, and added a third win at Oulton Park. After the round at Knockhill, Thompson was replaced by ex-Formula One driver Johnny Herbert due to clashes with his commitments in the WTCC and V8 Supercars.