At the outbreak of World War I Thomson learned to fly, being granted Royal Aero Club Aviators' Certificate No. 873 on 20 August 1914 after soloing a Bristol biplane at the Bristol School at Brooklands. He joined the Royal Naval Air Service as a probationary flight sub-lieutenant on 24 August, and was confirmed in his rank on 30 October, and posted to HMS Pembroke III. On 1 January 1915 he was promoted to flight lieutenant, seeing active service during the Gallipoli Campaign between April 1915 and January 1916, and on 14 March 1916 received a mention in despatches from the Vice-Admiral Commanding the Eastern Mediterranean Squadron, and also the award of the Distinguished Service Cross for his low altitudephotographic reconnaissance flights over enemy territory. On 30 June 1916 he was promoted to flight commander, and a year later, on 30 June 1917, to squadron commander. On 1 May 1918 Thomson was again mentioned in despatches "for zeal and devotion to duty during the period from 1 July to 31 December 1917". On 1 April 1918, Royal Naval Air Service was merged with the Army's Royal Flying Corps to form the Royal Air Force, and Thomson joined the new service with the rank of captain.. Soon after, the former No. 7 Squadron RNAS, now No. 207 Squadron RAF, was withdrawn from France to be re-equipped with the Handley Page O/400 heavy bomber at RAF Andover. On 24 May 1918 Thomson was appointed commander of No. 207 Squadron which returned to France on 7 June to be based at Ligescourt as part of No. 54 Wing of the Independent Air Force, to mount night-bombing operations. However his tenure was short as Thomson was promoted to the temporary rank of lieutenant colonel on 27 July, and transferred to command of No. 215 Squadron RAF. On 2 August 1918 Thomson was awarded the Distinguished Flying Cross. His citation read: Thomson left the RAF after the end of the war, being transferred to the unemployed list on 1 March 1919. On 19 July 1919 Thomson and his brother Captain Alexander Thomson were two of the ex-servicemen of the parish who were presented with silver-mounted walking sticks in recognition of their military service from the Parish Council of Effingham, where their father was a parish councillor, as part of the Peace Day celebrations marking the signing of the Treaty of Versailles which brought the war to an end. Thomson died at Staplehurst, Kent, at the age of 69.