Appleton was born in Bradford and educated at local schools and St John's College, Cambridge where he was awarded first class honours and several prizes in both parts of the Natural Sciences Tripos (1913, 1914). He began research at the Cavendish Laboratory, Cambridge with W.L. Bragg, but during his service in the Army Signals in the First World War he developed the interest in valves and 'wireless' signals which informed his subsequent research career. He returned to the Cavendish Laboratory in 1919, continuing to work on valves and, with B. van der Pol, on non-linearity, and on atmospherics. In 1924, in collaboration with M.F. Barnett, he performed a crucial experiment which enabled a reflecting layer in the atmosphere to be identified and measured; subsequent research indicated the existence of more than one reflecting layer. From 1924 to 1936 Appleton was Wheatstone Professor of Physics at King's College, London, directing research teams and, in 1932, heading an expedition to Tromsö in northern Norway as part of the programme of observations scheduled for the Second International Polar Year.

He was President of the International Union of Scientific Radio (URSI), 1934-1952. In 1936 he succeeded C.T.R. Wilson in the Jacksonian Chair of Natural Philosophy at Cambridge, where he continued collaborative research on many ionospheric problems, including solar and lunar tides in the E-layer. From September 1936 he served on the re-constituted Committee for the Scientific Survey of Air Defence (the 'Tizard Committee'), and in October 1938 was appointed successor to Sir Frank Smith as Secretary to the Department of Scientific and Industrial Research (DSIR). He remained at the DSIR throughout the Second World War and until 1948 when he was appointed Principal of Edinburgh University. He took up the appointment in May 1949 and remained in office until his death in 1965. Appleton was elected FRS in 1927 (Bakerian Lecture 1937, Hughes Medal 1933, Royal Medal 1950) and was awarded the Nobel Prize for Physics in 1947 for his investigations into the ionosphere. He was knighted in 1941.