While working as a high school English teacher, he wrote the book The 25th Hour and received positive recognition for the book. He later adapted the book into a screenplay, which was filmed starring Edward Norton and was directed by Spike Lee. He then wrote a collection of short stories titled When the Nines Roll Over (And Other Stories) in 2004.

Benioff drafted a screenplay of the mythological epic Troy (2004) for which Warner Bros pictures paid him $2.5 million. He also wrote the script for the psychological thriller Stay (2005). The film was released October 21, 2005, and was directed by Marc Forster and starred Ewan McGregor and Naomi Watts. His screenplay, The Kite Runner, a film based on the book bearing the same name, marked his second collaboration with director Marc Forster.

He wrote the screenplay for the X-Men spin-off X-Men Origins: Wolverine, he was hired for the project in 2004, working on the script for three years.

In 2008, his second novel City of Thieves, A Novel was released.

He is currently working on an adapted screenplay of the Charles R. Cross biography of the late Kurt Cobain, it is unknown if the screenplay has been developed. He is also working with D.B. Weiss as executive producer, showrunner and writer on Game of Thrones, HBO's adaptation of George R.R. Martin's A Song of Ice and Fire series of novels.