He graduated from Harvard University in 1960, attended Oxford University on a Rhodes scholarship, and earned a Ph.D. (D. Phil.) in history from Oxford in 1964, where he studied with Richard Cobb, among others. He worked as reporter at The New York Times from 1964 to 1965. He was awarded a MacArthur Fellowship in 1982, and was President of the American Historical Association in 1999.

He joined the Princeton University faculty in 1968, and was Shelby Cullom Davis Professor of European History. On July 1, 2007, he transferred to emeritus status at Princeton, and was appointed Carl H. Pforzheimer University Professor and director of the Harvard University Library, succeeding Sidney Verba. Princeton's Robert Darnton To Succeed Verba as Harvard Library Director - 5/25/2007 - Library Journal In 1983 he delivered the Huizinga Lecture in Leiden, the Netherlands, under the title The Meaning of Mother Goose.

Darnton is a pioneer in the field of the history of the book. He currently is writing about electronic publishing. He is founder of the Gutenberg-e program, sponsored by Mellon Foundation.

One of his books, The Forbidden Best-Sellers of Pre-Revolutionary France (New York: W.W. Norton, 1996), won the National Book Critics Circle Award for criticism in 1995.

In 1999 he was named a Chevalier of the Légion d'Honneur, an award given by the French government, in recognition of his work. In 2004 he was awarded the Gutenberg prize by the International Gutenberg Society.

In 2005 he received an award for distinguished achievement from the American Printing History Association. He was President of the American Historical Association from 1997-1998.

His brother is the retired New York Times editor and author John Darnton, and his father was the war correspondent Byron Darnton.