Wilson served with his regiment in the Second Boer War, where he took part in the relief of Ladysmith, including the battles of Spion Kop (January 1900) and the Tugela Heights (February 1900). On 24 August 1901 he was promoted to the rank of captain, and in April 1902 he was appointed a staff officer as an Assistant Provost-Marshal in South Africa. He stayed there until after the end of the war, leaving Cape Town on the SS "Orient" in October 1902. For his war service, he was mentioned in Despatches, and received the Queen's Medal with two clasps and the King's Medal with two clasps.