E. J. Bowen was the eldest of four born to Edmund Riley Bowen and Lilias Bowen (née Kamester) in 1898 in Worcester, England. He attended the Royal Grammar School Worcester.
He won the Brackenbury Scholarship in 1915 to the University of Oxford where he studied chemistry. In 1916, after less than a year of his undergraduate course, he volunteered for training as a gunner officer and served as Second Lieutenant in the Royal Garrison Artillery during World War I. After being demobilised in 1919, he returned to Balliol College.