He is the emeritus professor of the History of Christianity at the University of Cambridge, and a fellow and former president of Magdalene College.

He undertook postgraduate research at the University of Cambridge, where his doctoral advisers were Owen Chadwick and Gordon Rupp.

[5] His work has done much to overturn the popular image of late-medieval Catholicism in England as moribund, and instead presents it as a vibrant cultural force.

[6][7] On weekdays from 22 October to 2 November 2007, he presented the BBC Radio 4 series 10 Popes Who Shook the World[8] – those popes featured were Peter, Leo I, Gregory I, Gregory VII, Innocent III, Paul III, Pius IX, Pius XII, John XXIII, and John Paul II.

Duffy moved to Magdalene College in the University of Cambridge in 1979, and was professor of the history of Christianity from 2003 to 2014.