On leaving Oxford, he found employment in superintending some iron-works in South Wales, and married Harriette, daughter of Robert John Bunyon. McDougall and his wife Harriette (née Bunyon) sailed for Borneo via the Cape and Singapore on 30 December 1847, arrived in Sarawak on 29 June 1848 and was appointed the first Bishop of Labuan and Sarawak in 1849. He established a Medical mission there, and a 'Home School,' in which children were trained from infancy in the principles of Christianity. In 1853, he returned home in order to manage the transfer of the mission from the Borneo Mission Society, whose funds came to an end, to the Society for Propagating the Gospel. In 1854, he was back again in Sarawak. The work of the mission grew. McDougall was appointed bishop, of Labuan. He was consecrated at Calcutta on St. Luke's Day, 1855.