After his single seater career Thompson moved into the IMSA GT3 Cup Challenge for 2013. In a privately funded team, the driver scored two podium finishes. For 2014 Thompson signed with Kelly-Moss Motorsports. Winning three races (two at Watkins Glen and one at Road Atlanta, Thompson won the championship. Thompson made a guest appearance in the Porsche Supercup. At Circuit of the Americas, supporting the 2014 United States Grand Prix, Thompson failed to finish. For 2015 Thompson remained at Kelly-Moss Motorsports for a Pirelli World Challenge GT Cup campaign. Scoring thirteen class wins out of eighteen races, Thompson dominated the championship. The following year Thompson remained in the series but promoted to the GT class. Racing with the McLaren Automotive supported K-Pax Racing. His best result was a fourth place at Circuit of the Americas in his McLaren 650S.