Cowley led a group of five sisters in October 1897 from Strabane to South Africa as sister superior in response to an appeal from the bishop of Mahikeng, Dr Anthony Gaughran. They arrived in February 1898 and opened their first school. War broke out in October 1899, and Mahikeng was besieged. The convent was requisitioned to serve as a military hospital, with the sisters nursing the wounded. For seven months, the sisters lived in a bomb-proof shelter. Cowley was awarded the Royal Red Cross from King Edward VII on 1 October 1901 in recognition of her service during the war. She also received the South African War Medal.