Divenuto nel 1962 professore di Storia del Cristianesimo presso la Yale University di New Haven (Connecticut), nel 1972 è stato nominato Sterling Professor of History, ottenendo così una posizione di privilegio nel mondo accademico. In questo periodo Pelikan ha vinto diversi premi e riconoscimenti accrescendo notevolmente la propria fama di studioso: a culminare la propria attività, dal 1992 al 1993 ha tenuto una serie conferenze - dette Gifford Lectures - presso le quattro principali università della Scozia - St Andrews, Glasgow, Aberdeen e Edimburgo.
Pelikan ha scritto oltre trenta saggi sul Cristianesimo e la sua storia tra i quali spicca La Tradizione Cristiana: Storia dello sviluppo della dottrina (The Christian Tradition: A History of the Development of Doctrine), scritto tra il 1973 ed il 1990.
Elenco delle opere (titoli in Inglese)
Acts (2006) Brazos Press, ISBN 1-58743-094-0. A theological Bible commentary
Bach Among the Theologians (1986), Philadelphia: Fortress Press, ISBN 0-8006-0792-9
The Christian Tradition: A History of the Development of Doctrine, 5 vols. (1973–1990). Chicago: University of Chicago Press
Volume 1: The Emergence of the Catholic Tradition 100–600 (1973) ISBN 0-226-65371-4
Volume 2: The Spirit of Eastern Christendom 600–1700 (1974) ISBN 0-226-65373-0
Volume 3: The Growth of Medieval Theology 600–1300 (1978) ISBN 0-226-65375-7
Volume 4: Reformation of Church and Dogma 1300–1700 (1984) ISBN 0-226-65377-3
Volume 5: Christian Doctrine and Modern Culture since 1700 (1990) ISBN 0-226-65380-3
Christianity and Classical Culture: The Metamorphosis of Natural Theology in the Christian Encounter with Hellenism (1993) Gifford lectures at Aberdeen, Yale U. Press, ISBN 0-300-06255-9
Confessor Between East and West: A Portrait of Ukrainian Cardinal Josyf Slipyj
Credo: Historical and Theological Guide to Creeds and Confessions of Faith in the Christian Tradition (2003) Yale U. Press, ISBN 0-300-09388-8
Development of Christian Doctrine: Some Historical Prolegomena
Divine Rhetoric: The Sermon on the Mount As Message and As Model in Augustine, Chrysostom, and Luther (2000) St. Vladimir's Seminary Press, ISBN 0-88141-214-7
The Excellent Empire: The Fall of Rome and the Triumph of the Church
Sacred Writings: Buddhism – The Dhammapada (1987) Book of the Month Club, no ISBN
Sacred Writings: Hinduism – The Rig Veda (1992) Book of the Month Club, no ISBN
Sacred Writings: Islam – The Qur'an (1992) editor, Book of the Month Club, no ISBN, in English with Arabic sub-text
The World Treasury of Modern Religious Thought (1990), editor, hardcover: ISBN 0-316-69770-2, paperback: no ISBN issued
What Has Athens to Do with Jerusalem?: Timaeus and Genesis in Counterpoint (1998) Thomas Spencer Jerome Lectures, University of Michigan Press, ISBN 0-472-10807-7
Jesus Through the Centuries. His Place in the History of Culture, Yale University Press, 1999
Whose Bible Is It? A History of the Scriptures Through the Ages (2005) ISBN 0-670-03385-5