Writers Mike Werb and Michael Colleary wrote Face/Off as a spec script in 1990 after a mutual friend was injured in a hang-gliding accident, requiring their face to be removed, reconstructed, and reattached.

The screenplay originally had a futuristic setting and was inspired by the film White Heat, which features a plot where the main character survives a prison riot.

The project was optioned to Joel Silver and Warner Bros. in 1991, but the option expired in 1994 and was then purchased by Paramount Pictures.

Director Rob Cohen was originally attached to the film but left to direct Dragonheart (1996) when the project stalled in turnaround; John Woo became attached in 1996.

Various actor pairings were considered for the leads, including Sylvester Stallone and Arnold Schwarzenegger, Michael Douglas and Harrison Ford, and Alec Baldwin and Bruce Willis, before John Travolta and Nicolas Cage were cast.

Johnny Depp wanted to play Sean Archer but passed on the role after reading the script.

The names of the villain brothers, Castor and Pollux, reference Greek mythology, where the twins were transformed by Zeus into the constellation Gemini.

In preparation for directing, John Woo watched John Frankenheimer's 1966 film Seconds, which deals with a similar theme of identity and physical transformation.

Face/Off was the first film scored by composer John Powell, who was recommended to John Woo by Hans Zimmer after Zimmer said he was too busy to do it himself; Zimmer guaranteed he would fix the score if Powell failed, but ultimately did not need to intervene.

Powell had only ten weeks to compose 115 minutes of music for the film, with help from Gavin Greenaway on some sequences.

Principal photography began on January 4, 1997 in Los Angeles and wrapped on April 1, with the climactic boat chase scene filmed in San Pedro.

Face/Off is considered part of the 'holy trinity' of Nicolas Cage action films from the 1990s, alongside Con Air (1997) and The Rock (1996).

Face/Off is said to have inspired the Hong Kong film Infernal Affairs, though director Andrew Lau opted for a more realistic identity swap instead of a physical face change; Infernal Affairs later inspired Martin Scorsese's The Departed.