Thomson first came to prominence when he won the Boys Amateur Championship at Glasgow Golf Club in 1931, beating Francis McGloin 5&4 in the final.

In 1936 he won the Amateur Championship, beating the Australian Jim Ferrier by 2 holes in the final.

The same year he played in the Walker Cup losing 10½–1½ to the Americans, a match in which the British team only got three halves.

Thomson gave up his amateur status in late 1939 to work in his father's golf school.

His situation was complicated by the fact that he worked for his father and was not affiliated to a golf club.