Robert Charles Zaehner was born on 8 April 1913 in Kent. He attended Christ Church, Oxford, from 1933 to 1937, where he studied Greek, Latin, Persian and Avestan, eventually obtaining first class honours in oriental languages. His expertise in this area led to his being recruited by the British Special Operations Executive during World War II. He served in the British embassy in Tehran from 1943 to 1947, during which time he adopted the Catholic faith which was to shape much of his later work. His career in civil service also continued to be closely linked to his academic career for some time.

From 1947 to 1949, he remained in Britain, conducting research as well as working with MI6. In 1949 he was sent to Malta to train Albanians for anti-Communist combat. His 1950 appointment to a lectureship in Persian at Oxford was suspended for a time between 1951 and 1952, when a diplomatic crisis mandated his return to Tehran.

Upon returning to Oxford in 1952, Zaehner was appointed to the Spalding Professorship of Eastern Religions and Ethics, his ambivalence towards which he recounts in the introductory chapter of Concordant Discord. He held the post until his death on 24 November 1974. Zaehner never married.

His publications include Zurvan: A Zoroastrian Dilemma (1955), Mysticism: Sacred and Profane (1957), Concordant Discord (1970), Evolution in Religion (1971), Our Savage God(1974) and The City within the Heart (1980).