FitzGerald became a journalist, initially writing for the "New York Herald Tribune" magazine. She went to South Vietnam in January 1966. She met Washington Post journalist Ward Just at a party soon after arriving in Saigon and began a relationship with him that continued until she left South Vietnam in November 1966. She formed a close connection with Daniel Ellsberg who was working as an intelligence officer at the U.S. Embassy. Unlike many male journalists, she didn't report on the latest combat operations, but rather focussed on the effects of the war on South Vietnamese politics and society. Her first article titled "The Hopeful Americans & the Weightless Mr. Ky" was published in the "Village Voice" on 21 April 1966. She investigated the effects of Operation Masher on South Vietnamese civilians and followed the Buddhist Uprising. She repeatedly visited the village of Duc Lap, interviewing villagers to write "Life and Death of a Vietnamese Village" which appeared in "The New York Times Magazine" on 4 September 1966. Her final story was "Behind the Facade: the Tragedy of Saigon" describing the conditions of refugees who had sought safety in the city and were overwhelming its inadequate infrastructure and funding.