Stone received Guggenheim and National Endowment for the Humanities fellowships, the five-year Mildred and Harold Strauss Living Award, the John Dos Passos Prize for Literature, and the American Academy and Institute of Arts and Letters Award. He also taught at the creative writing program at Yale University.

Fiction

In 1967 Stone published his first novel, A Hall of Mirrors, which won both a Houghton Mifflin Literary Fellowship, and a William Faulkner Foundation award for best first novel. Set in New Orleans in 1962 and based partly on actual events, the novel depicted a political scene dominated by right-wing racism, but its style was more reminiscent of Beat writers than of earlier social realists: alternating between naturalism and stream of consciousness, with a large cast of often psychologically unstable characters, it set the template for much of Stone's later writing. It was adapted into the 1970 film WUSA. The novel's success led to a Guggenheim Fellowship and began Stone's career as a professional writer and teacher.

In 1971 Stone traveled to Vietnam as a correspondent for a British journal. His time there served as the inspiration for his second novel, Dog Soldiers (1974), following a journalist smuggling heroin from Vietnam. It won the 1975 National Book Award, and was also adapted into a film, Who'll Stop the Rain.

A Flag for Sunrise (1981) further developed Stone's trademark brand of acid-tinged existential realism while continuing to explore broad political and social questions as in his first two novels. The story follows a wide cast of, mostly aimless, characters as their paths intersect in a fictional Central American country. Catalyzing the crises of belief faced by each character is a backdrop of violent political struggle between a U.S.-backed dictator and almost equally corrupt Marxist revolutionaries. The novel won the PEN/Faulkner Award. Stone's next two novels focused on smaller-scale conflicts: the psychotic breakdown of a movie actress in Children of Light, and a circumnavigation race in Outerbridge Reach (based loosely on the story of Donald Crowhurst). He returned to current events with Damascus Gate (1998), about a man with messianic delusions caught up in a terrorist plot in Jerusalem.

Non-fiction

Prime Green: Remembering the Sixties (2007) is Stone's recent memoir discussing his experiences in the Sixties "counterculture". It demonstrates Stone's knowledge and insight into a turbulent decade. The autobiographical work begins with his days in the Navy and ends with his days as a correspondent in Vietnam. The work features Stone's insights on Neal Cassady, Allen Ginsberg, and Jack Kerouac from his time spent traveling with them. Stone offers a candid look at sixties drug culture including the use of marijuana, LSD, heroin, and peyote.