In 1900 FitzGerald joined the imperial yeomanry to fight in the South African War, where he received a commission as second lieutenant in the 5th dragoon guards, and first lieutenant in 1901. He was later transferred to the 6th (Inniskilling) Dragoons, and was promoted captain in 1906, and major in 1912. He was employed in the War Office from 1914 to 1919. In 1903 he stopped climbing after an accident in Zermatt and married traveller and author Ménie Muriel Dowie (1866–1945).