Danner was born at Utica, New York. He studied modern literatures and aesthetics at Harvard. After graduating in 1981, he joined the staff of The New York Review of Books
In 1984, Danner joined Harper's Magazine as senior editor. In 1986, he joined The New York Times Magazine, where he stayed for four years.
In 1990, Danner joined the staff of The New Yorker shortly after the magazine published his three-part series on Haiti, "A Reporter At Large: Beyond the Mountains".
On December 6, 1993, for only second time in its history, The New Yorker devoted its entire issue to one article, Danner's piece, "The Truth of El Mozote", an investigation into the El Mozote massacre in El Salvador, thought to be the worst atrocity in modern Latin American history. The Mozote article became the basis for Danner's first book, The Massacre at El Mozote: A Parable of the Cold War, which was published in 1994.
Danner's second book, The Saddest Story: America After the Cold War, which appeared in 1999, was based an series of articles he wrote on the war in Yugoslavia. In 1999, he was also awarded a MacArthur Fellowship.
Danner's third book, a study of Haiti entitled Beyond the Mountains: The Legacy of Duvalier, is was published in 2000.
Danner co-wrote and helped produce two hour-long television documentaries for ABC News' Peter Jennings Reporting series: While America Watched: The Bosnian Tragedy and House on Fire: America's Haitian Crisis, which both aired in 1994. As commentator, Danner has appeared on The Charlie Rose Show and The MacNeil-Lehrer NewsHour on PBS, CNN's Prime News, ABC's World News Now, and C-Span's Morning Show.
Danner also teaches journalism at the University of California, Berkeley and Bard College.