In 1940, Fergusson was serving as a brigade major for the 46th Infantry Brigade before becoming a general staff officer in the Middle East. In October 1943 he was promoted to acting brigadier and given command of the 16th Infantry Brigade, which was converted into a Chindit formation for operations in the deep jungles of Burma miles behind Japanese lines. He commanded this brigade throughout the Chindit operations of 1944 before becoming Director of Combined Operations from 1945 to 1946. He ended the war as a major (war-substantive lieutenant-colonel).