Mostow helmed several short films and documentaries as well as music videos before making his first feature, the direct-to-video release Beverly Hills Bodysnatchers (1989). He then made the Showtime film Flight of Black Angel (1991), about a colonel who trains fighter pilots and his troubled protégé who wants to attack the local population.

In 1997 Mostow directed Breakdown. The thriller stars Kurt Russell as a man whose wife seems to have vanished in the desert. Mostow went on to co-found a production company with former executive Hal Lieberman and signed a four-year deal with Universal. He also spent several years developing The Game (1997), but opted instead to direct his own original screenplay for Breakdown. Mostow was credited as Executive Producer on the David Fincher-directed film.

Mostow and Michael Douglas (who starred in The Game) were to collaborate on a World War II-era submarine film U-571 (2000) but Douglas pulled out due to scheduling conflicts. Instead, the Director assembled a cast including Harvey Keitel, Bill Paxton, Matthew McConaughey, Jack Noseworthy, Matthew Settle and Thomas Guiry for U-571, a film about an attempt by the USA to intercept a German U-boat carrying a coding device. Loosely based on fact (although it really involved British forces, not Americans), the film earned $77 million in domestic receipts. The film was nominated for two Academy Awards, and won the Oscar for Best Sound Editing. At the time of its release, British Prime Minister Tony Blair condemned U-571 in parliament as an insult to the Royal Navy. The Guardian newspaper called the film 'tasteless' and opined that the British sailors memories had been 'desecrated'.

In 2003 Mostow directed the third installment of The Terminator series, Terminator 3: Rise of the Machines. The film performed below industry expectations and failed to duplicate the critical reception of its predecessors, yet was still a commercial success, grossing over $433,371,112 at the worldwide box-office.

After a six-year absence, Mostow returned to direct another film, Surrogates, based on the comic book series and starring Bruce Willis. The film was released into cinemas on September 25, 2009 to mixed reviews. Mostow wrote the story of the horror thriller House at the End of the Street (2012).