During World War II, Thompson served in the Royal Canadian Air Force (RCAF). He was also the coach of the Calgary RCAF Mustangs of the Alberta Senior Hockey League. He led the Mustangs to the league championship series in 1942–43 against the Calgary Currie Army team. In March 1943, injuries to the Mustangs' goaltenders made him play again. With Thompson in goal, the Mustangs won against Currie Army, 8–4, to tie the best-of-five series at two wins each. He played the deciding game, but his team fell short of winning the Alberta title with a 3–1 loss.