After graduating from the Royal Military Academy, Woolwich, in 1894, Thomson was commissioned into the Royal Engineers. He served first in Mauritius and then saw action during the Second Boer War (1899–1902) during which he was in command of a field company section and was mentioned in dispatches. He also had his first encounter with aviation when he was detailed to help with the RE Balloon Section outside Kimberley. After the war he became an instructor at the School of Military Engineering at Chatham and then at Sierra Leone. He was promoted to captain and brevet major in 1904 and in 1909 joined the Army Staff College in Camberley. In 1911 he went to the War Office, and in 1912 Thomson was appointed military attaché with the Serbian army during the first and Second Balkan Wars, after which he returned to the War Office in 1913.