Boxer returned to London for a two-year posting from 1935–36 to the military intelligence section of the War Office. Posted to Hong Kong in 1936, he served as a General Staff Officer 3rd grade (GSO3) with British troops in China at Hong Kong, doing intelligence work. Between 1937 and 1941, Boxer, promoted from captain to major, became one of the key members of the Far East Combined Bureau, a British intelligence organisation that extended from Shanghai to Singapore. By 1940, most of its Hong Kong office had been transferred to Singapore, leaving Boxer as the army's chief intelligence officer in the colony. In 1940, he was advanced to General Staff Officer 2nd grade (GSO2). Wounded in action during the Japanese attack on Hong Kong on 8 December 1941, he was taken by the Japanese as a prisoner of war and remained in captivity until 1945. After his release, Boxer returned to Japan in February 1946 as a member of the British Far Eastern Commission, a post that he served until the next year. During his military career, Boxer published 86 publications on Far Eastern history with a particular focus on the 16th and 17th centuries.