John Thomson joined the Arlington Baths Club in Glasgow as a junior member in 1916. He was the Scottish junior freestyle champion in 1920, and in 1922 won the Western Counties 100 and 200 yards freestyle titles. That same year he established a Scottish 300 yards record of 3:51.0. The following year (1923) Thomson was the Scottish 220 champion and also won the Western Counties 100, 220 and 440 titles. In addition he won the Western Counties Water Polo Cup with Arlington. Thomson enjoyed a memorable year in 1924, winning the Scottish 220 title and setting Scottish records for the 300 yards (3:46.4) and 220 yards (2:33.0). He also competed at the Paris Olympics finishing fifth as a member of the British 4 x 200 metres freestyle relay squad. Thomson added the 1925 Western Counties 100 yards title to his collection and in 1927 won the Scottish 100 yards title. His final title was in 1930, as a member of the Arlington squad that won the Scottish Team Championship for the fifth time since 1924 . An engineer by trade, Thomson was made a life member of the Arlington Baths in 1943.