Educated at Clifton College, he was commissioned into the Scots Guards as a second lieutenant on 29 December 1888, promoted to lieutenant on 13 April 1892, and to captain on 24 June 1899. When the Second Boer War broke out in October 1899, the 1st battalion of the Scots Guards departed Ireland for South Africa to join up with the 1st Guards Brigade, with Lowther appointed adjutant. They reached that country in November, and immediately saw action in the battles of Belmont and Modder River, both British victories, though at a heavy cost in British life. In December, the battalion was present at the Battle of Magersfontein, and the following year took part in the march to take the Boer capitals of Bloemfontein and Pretoria. After taking the latter city, the 1st Guards Brigade took part in the Battle of Diamond Hill (June 1900), and in the last large scale battle of the war at Bergendal in August 1900. The war then became a guerrilla war, and Lowther was on 20 July 1901 appointed to a staff position as Staff Captain for Intelligence. For his service in the war, Lowther received the Queen's South Africa Medal, was appointed a Companion of the Distinguished Service Order (DSO), and was noted for future staff employment.