After attending the University of Wisconsin—Madison, Darnton joined The New York Times as a copyboy in 1966. Two years later he became a reporter and for the next eight years he worked in and around New York City, including stints as the Connecticut correspondent, during the Black Panther trials in New Haven, and as a City Hall reporter in the Lindsay and Beame Administrations. In 1976 he went abroad as a foreign correspondent, first covering Africa out of Lagos, Nigeria, and then, when the military government there expelled him in 1977, out of Nairobi, Kenya. He covered protests in South Africa, liberation movements in Rhodesia, guerrilla fighting in Ethiopia, Somalia, Zaire and elsewhere and the fall of Idi Amin in Uganda. His work in Africa earned him the 1978 George Polk Award. In 1979, he covered Eastern Europe for the Times, based in Warsaw, Poland, and he received both the Polk Award and the 1982 Pulitzer Prize for Journalism for his coverage of Poland under martial law when he smuggled stories out of the country. He went on to become the bureau chief in Madrid and London and also served as the deputy foreign editor, the metropolitan editor and the cultural news editor at the Times. He retired from the Times in 2005.

In 1996, Darnton published his first novel, Neanderthal. The novel, which received a number of positive reviews and was well-received, became a bestseller overnight. Since his first success, Darnton has continued his career, publishing mostly thrillers with much scientific and historical detail. His 2005 novel, The Darwin Conspiracy, deals with Victorian era England.His next novel, Black and White and Dead All Over, is a satirical roman à clef about a string of murders at a newspaper suspiciously like the New York Times.

He recently taught at the State University of New York at New Paltz. In 2009, John Darnton was named curator of the George Polk Awards.

Darnton is a son of Byron Darnton, a New York Times war correspondent who was killed in New Guinea in 1942 during World War II. His brother is the cultural historian Robert Darnton.

Darnton and his wife, the journalist Nina Darnton, live in New York City. They have two daughters, Kyra and Liza, and a son, Jaime.

Novels

• Neanderthal (1996)
• The Experiment (1999)
• Mind Catcher (2002)
• The Darwin Conspiracy. (2005)
• Black & White and Dead All Over (2008)