Singer was born in New York City. He was adopted by Norbert and Grace Singer and grew up in a Jewish household in New Jersey. He attended West Windsor-Plainsboro High School South (formerly just West Windsor-Plainsboro High School), then studied filmmaking at New York's School of Visual Arts and later the USC School of Cinematic Arts in Los Angeles. Actors Lori and Marc Singer are his cousins. He is Jewish and openly gay, and has said that his life experiences of growing up as a minority influenced his movies.

His production company, Bad Hat Harry Productions, produces House and works in television, film, and video game media. It is named after a line from Jaws, one of his favorite films. The line, "That's some bad hat, Harry", is heard over the company's end credit animation.

After graduating, Singer directed a short film called Lion's Den. With Lion's Den, he involved a number of friends, including actor Ethan Hawke whom he knew from his childhood in New Jersey and editor John Ottman who he had met while working on a friend's short film.

After a screening of Lion's Den, Singer was approached by someone who knew of a Japanese company that funded low-budget films. Singer wrote the concept with high school friend Christopher McQuarrie, fellow USC alumn Michael Feit Dougan wrote the first draft in ten days. The movie about a supposedly idyllic small town. Ottman again served as editor but this time also composed the score for the film. At the 1993 Sundance Film Festival the film was named as co-winner of the Grand Jury Prize.

While attending the 1993 Sundance Film Festival, Singer and McQuarrie began discussing an idea that McQuarrie had for a story where "five criminals meet in a police line-up". The film, The Usual Suspects, won a number of awards including the 1995 BAFTA Award for Best Film and Saturn Award for Best Action/Adventure/Thriller Film. Writer McQuarrie won the Academy Award for Writing Original Screenplay and the BAFTA Award for Best Screenplay, composer/editor Ottman won the BAFTA Award for Best Editing and the Saturn Award for Best Music and actor Kevin Spacey won the Academy Award for Best Supporting Actor.

In 1998, Singer directed Apt Pupil, from a screenplay written by Brandon Boyce, another of his friends. The story, adapted from a Stephen King novella of the same name (collected in the book Different Seasons), tells of a young boy who develops a morbid fascination with a Nazi war criminal. An experience from Singer's childhood, where he and his friends briefly formed a "Nazi Club", is often cited as attracting him to this project (Singer said this club was born not out of anti-Semitism but rather due to the kids' fascination with World War II).

Singer was initially approached by 20th Century Fox to direct X-Men after directing The Usual Suspects, but not being a fan of comics and being unaware of the characters, Singer turned them down. However his friend, Tom DeSanto, a big fan of the comics and partner in his production company Bad Hat Harry Productions, eventually persuaded Singer to reconsider and, after reading the comics and becoming familiar with the characters, Singer signed on to direct. Rejecting all the scripts and storylines that were developed over a decade of failed production attempts, Singer developed the story for the film with DeSanto in a week and then worked on the script with a friend who had actually started out as Singer's driver, David Hayter. Singer won the 2000 Saturn Award for Best Direction for X-Men.

In early 2001, Singer was planning to direct Confessions of a Dangerous Mind with Johnny Depp in the lead role, from Charlie Kaufman's script based on the Chuck Barris book of the same name. However financial troubles delayed production and Singer had to move on. The film was later directed by George Clooney for Miramax Films with Sam Rockwell in the lead role. Singer has said that he was "very impressed" by Clooney's direction, and the film itself.

In late 2001, Singer was planning to help DeSanto produce a new Battlestar Galactica television series for Studios USA (now NBC Universal Television Studio) and the FOX network. Singer was scheduled to direct the mini-series which would have served as a backdoor pilot for a potential series. Speaking to Variety in February 2001, Singer said he was "confident that the Galactica brand is a sleeping giant. It was a show I watched during its initial run, from the pilot to the final episode. The essence and the brand name is quite potent in a climate where there's a great deficit of sci-fi programming." Despite his enthusiasm, production delays caused by the September 11, 2001 attacks meant Singer had to drop out due to his commitment to direct X-Men 2. FOX then lost interest in Galactica and Studios USA took the project to the Sci Fi Channel and a different production team. This resulted in the new Battlestar Galactica 2003 mini-series and 2004 television series.

In June 2002 filming began on X2 in Canada with Singer again directing, this time from a screenplay written by David Hayter, Dan Harris and Michael Dougherty. In 2004, X2 was nominated for the Hugo Award for Best Dramatic Presentation, Long Form, but lost to Peter Jackson's The Lord of the Rings: The Return of the King.

In 2002 having learned that Singer was a life long Star Trek fan, Patrick Stewart arranged for Singer to visit the set of Star Trek: Nemesis and appear in the finished film as a Starfleet officer on the bridge of the Enterprise.

On November 16, 2004 a new medical drama debuted on FOX called House, M.D. (shortened to House), with Singer attached as an executive producer. He also directed the pilot and the third episode, then appeared in a brief cameo as himself in the twelfth episode.

As an elaborate joke, during the final days of principal photography, Singer was called into New Zealand by director Peter Jackson to "direct" some of the last few shots of his remake of King Kong, the reason being that Jackson was exhausted from weeks of work and needed to sleep, but also needed to assure the Universal executives that progress was in fact being made. Part of these proceedings were shown on Peter Jackson's King Kong Production Diaries, as well as on the Bryan Singer's Production Journals.

In mid-2004, Singer was in negotiations to direct X-Men 3 for Fox, but he was then offered the chance to direct the new Superman film. On July 19, 2004, Variety reported that Singer had signed on to direct Superman Returns for Warner Bros.. In retaliation, Fox terminated their production deal with Bad Hat Harry Productions, Singer's production company. Superman Returns was filmed in Australia in 2005, and was released on June 28, 2006. Singer claims that though he had not read the comics, he had always admired and identified with the character, citing the fact that he and Superman are both orphans. He instead based Returns on his love of the 1978 film made by Richard Donner.

Before embarking on the Superman sequel, Singer openly discussed helming a smaller project going back to the days of thrillers The Usual Suspects and Apt Pupil. In late 2006, screenwriter Christopher McQuarrie presented to Singer a story that took place in World War II. In the following months, the two collaborated on the project, an original thriller that would be a multi-character ensemble piece. In March 2007, the duo brought the project directly to United Artists partners Paula Wagner and Tom Cruise, who immediately agreed to finance the film. The script is based on the actual events of German generals plotting to assassinate Adolf Hitler during World War II. Singer invited Tom Cruise to take the lead role, which Cruise accepted. Filming will begin on July 19 in Berlin.

Upon finishing Valkyrie at the end of the year, Singer will jump directly into the upcoming Superman sequel (rumored title: The Man of Steel) which will begin filming around March 2008. Attending the recent Saturn Awards along with Superman Returns writers Michael Dougherty and Dan Harris and producer Gil Adler, Singer confirmed that the story had been locked down, and the first draft would be completed near the end of the year. Among the plans for the sequel include more action sequences, an alien villain, and Singer's promise to "go all Wrath of Khan on it" - a reference to Star Trek II: The Wrath of Khan. The film is scheduled for release in Summer 2009.