Wynne served in the Second Boer War and was made Deputy Adjutant-General for the Natal Field Force in South Africa, and after the Battle of Spion Kop he was given command of the 11th Infantry Brigade in place of General Edward Woodgate, who had been killed. During the Battle of the Tugela Heights in February 1900 Wynne was himself slightly injured, and his command was given to Colonel Walter Kitchener. After recovering, he was appointed in command of the Cape Colony District until his return to the United Kingdom in early 1902. He was mentioned in despatches (including by Lord Kitchener, dated 23 June 1902).