His first feature film was the John Woo-produced action film The Replacement Killers (1998), starring Chow Yun Fat. He then directed the crime thriller Training Day (2001), for which star Denzel Washington won an Academy Award for Best Actor. His next films were the action war drama Tears of the Sun (2003), the Arthurian legend film King Arthur (2004), the conspiracy action thriller Shooter (2007), the crime film Brooklyn's Finest (2010), and the action thrillers Olympus Has Fallen (2013) and The Equalizer (2014), the latter of which pairs Fuqua with Denzel Washington again. His most recent film is the action Western The Magnificent Seven (2016).

In 1998, Actress Lela Rochon and he were engaged, and they married on April 9, 1999. Daughter Asia Rochon Fuqua was born on July 28, 2002, followed by son Brando in May 2004. Fuqua has a son, Zachary, from a previous relationship.

In 2010, CBS Films hired Fuqua to direct a new movie based on a Vince Flynn novel, Consent to Kill. In May 2014, 20th Century Fox set Fuqua to direct a drug-smuggling thriller film Narco Sub, which is scripted by David Guggenheim.

In March 2011, Fuqua signed on to direct a film featuring the romantic love story between Consort Yang Yuhuan and Emperor Xuanzong of the Tang dynasty. As reported in March 2013, he has stated that he was awaiting the film project to go through the appropriate Chinese government channels before directing the historical epic film, currently known as The Tang Dynasty.

When asked by the BBC in September 2014 if he believes in God, Fuqua said: "Absolutely. I believe in God, absolutely."

In 2016, Fuqua directed The Magnificent Seven, a remake of the 1960 Western of the same name and Akira Kurosawa's Seven Samurai, on which the Western was based. This was the third of Fuqua's films starring Denzel Washington, who plays the lead role of Sam Chisolm. He was also the executive Producer of the 2016 television remake of Roots.