When the British Isles tour ended, Crean decided to stay on in South Africa, working as a doctor in a hospital in Johannesburg and playing rugby for Johannesburg Wanderers. In 1899, at the start of the Second Boer War, he enlisted as a trooper in the Imperial Light Horse and took part in both the Relief of Mafeking and the Relief of Ladysmith. On 26 October 1899, according to the "Irish Times", the Imperial Light Horse particularly distinguished themselves in the Battle of Elandslaagete. The "Irish Times" of the following day reported with regret that the list of wounded included Crean. It was during this engagement that Crean's former Wanderers and British Isles' teammate Robert Johnston won his Victoria Cross. In 1901, he became a Surgeon Captain and on 18 December, at the Battle of Tygerkloof, he won his VC when he successfully attended the wounds of two soldiers and a fellow officer under heavy enemy fire. The citation read: