Moores commissioned into the Royal Army Medical Corps as surgeon-captain on 1 February 1890, and served in the Chitral Relief Expedition in 1895, in medical charge of the 1st Battalion Gordon Highlanders and No. 8 Mountain Battery Royal Artillery. He served in the Second Boer War in South Africa (1899–1902), attached to the Scots Guards taking part in the Kimberley relief force, and was present at the battles of Belmont, Enslin and Modder River (November 1899), where he was wounded. For his service, he was promoted to surgeon-major on 29 November 1900, and twice mentioned in dispatches. Following the end of the war, Moores left Cape Town for England on the "SS Simla" in July 1902.