The short films that he has written the screenplays for include Kofi (2003) and Victoria para chino (2004).
He wrote the screenplay to his feature film, Sin Nombre (2009), as well as his segment for the omnibus film, Chinatown Film Project (2009).
He was an executive producer on Andrew Okpeaha Mac Lean's feature film thriller, On the Ice, which won "Best Debut Film" and the "Crystal Bear" (Best Feature Film for the Generation 14 ) at the 2011 Berlin Film Festival, among other awards.
Fukunaga served as an executive producer for the HBO series he directed, True Detective. chose Fukunaga to develop, direct, and write its adaptations of Stephen King's It (2017), the first of which was initially due to start shooting in summer 2015.
Fukunaga was originally slated to direct the 2018 TNT TV series The Alienist.