During the Battle of Sari Bair of August 1915, during which the New Zealanders attacked Chunuk Bair, the assistant director of medical services of the New Zealand and Australian Division, Colonel Neville Manders, was wounded and Begg took over his duties. He immediately set about dealing with the backlog of wounded soldiers that had accumulated at the beach. Shortly after completing this task, he became ill with gastro enteritis. Initially evacuated to Malta, he was sent to England for further treatment. He returned to Gallipoli on 12 November and was made the acting director of medical services. Promoted to temporary colonel, he helped with the organisation of the evacuation of Allied forces from Gallipoli the following month. His services at Gallipoli were recognised with a mention in despatches and he was made a Companion of the Order of St. Michael and St. George.