Prowse served in the Second Boer War from 1899 to 1902, by which time he had regained the rank of lieutenant. He was seconded to the army's railway staff on 16 June 1900 and was mentioned in despatches by Field Marshal Lord Roberts on 8 February and 4 September 1901. During the war he served as a staff officer and was present at the Relief of Ladysmith and at the battles of Spion Kop, Vaal Krantz and the Tugela Heights, serving also in Natal, Transvaal, the Orange River Colony, and the Cape Colony, and receiving the Queen's Medal with five clasps and the King's Medal with two. He was his battalion's adjutant by 14 August 1901 when he was promoted to captain.