Three months before the outbreak of the Second Boer War Henderson was posted to Natal as an intelligence officer. During the opening stage of the war he took part and was wounded at the Siege of Ladysmith. He received a brevet promotion to lieutenant-colonel on 29 November 1900. In February 1901, the commander-in-chief in South Africa, Lord Kitchener, appointed Henderson his director of military intelligence, a post he held until the end of the war in June 1902. In a despatch dated 23 June 1902, Kitchener wrote how Henderson had "invariable done his best to cope with the great difficulties of his position." For his service in the war, he was awarded the Distinguished Service Order (DSO) in the October 1902 South Africa Honours list. His subsequent works, "Field Intelligence: Its Principles and Practice" (1904) and "The Art of Reconnaissance" (1907), did much to establish his reputation as the Army's authority on tactical intelligence.