Following the outbreak of the Second Boer War in late 1899, the 2nd battalion Scots Guards were posted to South Africa as reinforcements in April 1900.

Paynter served there with the battalion until the end of the war, and took part in operations in the Orange River Colony from May to November 1900, including the actions at Biddulphsberg (May 1900) and in the Wittebergen (July 1900).

[2] The war ended with the Peace of Vereeniging in June 1902, and Paynter left Port Natal with other men of the 2nd Battalion Scots Guards on the SS Michigan in late September 1902, arriving at Southampton in late October, when the battalion was posted to Aldershot.

Paynter was awarded the Distinguished Service Order for his leadership of the 2nd Battalion, Scots Guards in fighting on 24 October 1914.

While staying at the castle Paynter had a relationship with one of the nurses, who was subsequently fired by Almina Herbert, Countess of Carnarvon.