Charles Ralph Boxer was born on March 8, 1904, in Sandown, Isle of Wight, England, to Hugh Edward Richard Boxer and Jane Patterson. He attended Wellington College from 1918 to 1921 and the Royal Military College, Sandhurst, from 1922 to 1923. In 1924, Boxer began his military service by joining the Lincolnshire Regiment. From 1930 to 1933, he was seconded to a regiment of the Imperial Japanese Army, an experience that stimulated his scholarly interest in East Asian cultures and history and impacted his later academic career. Before the start of World War II, Boxer made his mark in academic circles by publishing over eighty scholarly works. On June 8, 1939, he married Ursula Norah Anstice Tulloch (1909-1996), and Boxer was stationed in Hong Kong from 1939 to 1941 to serve as chief of army intelligence. While in Hong Kong, Boxer fell in love with the American feminist writer Emily (Mickey) Hahn (1905-1997). In December 1941, the Japanese invaded Hong Kong and took Boxer as a prisoner of war until the conclusion of World War II. The Japanese military also confiscated his prized rare book collection and transferred it to the Imperial Library; Boxer later recovered most of his library. In 1945, Boxer divorced Tulloch as a result of his widely publicized love affair, and he married Hahn in New York on November 28. Boxer retired from the army at the rank of major in 1947 and moved his family to the family estate in Broadmayne, Dorset, England.

Shortly after the end of his military career, Boxer was offered the Camoens chair of Portuguese in King's College London, which he accepted and held until his retirement from King's College in 1967, excepting a three-year period (1951-1953) when Boxer was professor of history of the Far East in the School of Oriental and African Studies, London. In 1955, Boxer moved to Little Gaddesden, Hertfordshire, England, which remained his permanent place of residence until his death. From 1967 to 1972, Boxer was simultaneously a research professor at Indiana University and professor of the history of the expansion of Europe at Yale University. In 1972, he retired from Yale as professor emeritus and continued to teach at Indiana University for seven more years. His initial research interests concerned early contact between Europeans, particularly the Dutch, the Portuguese, and Jesuit missionaries, and Japan, but Boxer later expanded his field of study to international history more broadly. He was a prolific writer and scholar, authoring about 350 books and articles. Boxer received many honors for his work, including election to the British Academy in 1957 and various honorary degrees and fellowships. King's College, London's Charles Boxer chair of history was established in his honor. Boxer passed away on April 27, 2000, in St. Albans, Hertfordshire, England, at the age of 96.