Theroux was born in Singapore, the son of American travel writer and novelist Paul Theroux and his English then-wife, Anne Castle. His paternal grandmother, Anne, was Italian American, and his paternal grandfather, Albert, was French-Canadian. He holds dual British and American citizenship. His older brother, Marcel, is a writer and television presenter, while his cousin, Justin, is an actor and screenwriter. He is the nephew of novelist Alexander Theroux and writer Peter Theroux.
Theroux moved with his family to Britain at the age of one, and was brought up in London thereafter. He was educated at Westminster School, a public school within the precincts of Westminster Abbey. While there he became friends with comedians Adam Buxton and Joe Cornish, and the Liberal Democrat politician Nick Clegg (with whom he travelled to America). He also performed in a number of school theatre productions including Bugsy Malone as Looney Bergonzi, Ritual for Dolls as the Army Officer, and The Splendour Falls as the Minstrel. After Westminster, Theroux read Modern History at Magdalen College, Oxford from 1988 to 1991, attaining first-class honours.
Theroux's first employment as a journalist was in the United States with Metro Silicon Valley, an alternative free weekly newspaper in San Jose, California. In 1992, he was hired as a writer for Spy magazine. He also worked as a correspondent on Michael Moore's TV Nation series, for which he provided segments on off-beat cultural subjects, including selling Avon to women in the Amazon Rainforest, the Jerusalem syndrome and attempts by the Ku Klux Klan to rebrand itself as a civil rights group for white people.
When TV Nation ended, Theroux was signed to a development deal by the BBC, through which he developed Louis Theroux's Weird Weekends. He has guest-written for a number of publications including Hip Hop Connection, and he continues to write for The Idler.
In Weird Weekends (1998–2000), Theroux followed marginal, mostly American subcultures such as survivalists, black nationalists, white supremacists and porn stars, often by living among or close to the people involved. Often, his documentary method subtly exposed the contradictions or farcical elements of some seriously held beliefs. Theroux describes the aim of the series as:
"Setting out to discover the genuinely odd in the most ordinary setting. To me, it's almost a privilege to be welcomed into these communities and to shine a light on them and, maybe, through my enthusiasm, to get people to reveal more of themselves than they may have intended. The show is laughing at me, adrift in their world, as much as at them. I don't have to play up that stuff. I'm not a matinee idol disguised as a nerd."
In the series When Louis Met... (2000–02), Theroux accompanied a different British celebrity in each programme in their daily lives, interviewing them as they go. His episode about British entertainer Jimmy Savile, When Louis Met Jimmy, was voted one of the top documentaries of all time in a 2005 survey by Britain's Channel 4. Some years after the episode was filmed, NSPCC described Savile as one of the most prolific sex offenders in Great Britain.
In an interview in 2015, Theroux expressed his intention to produce a follow-up documentary about Savile for the BBC to explore how the late entertainer had continued his abuse for so long, and to meet people he knew closely, and to examine his own reflections on his inability to dig more deeply in the first case. This follow-up documentary, with the title Savile, aired on BBC Two on Sunday 2 October 2016 and lasted 1 hour, 15 minutes.
In When Louis Met the Hamiltons, the former Conservative MP Neil Hamilton and his wife Christine were arrested during the course of filming, due to false allegations of indecent assault.
In When Louis Met Max Clifford, Max Clifford tried to set up Theroux, but he was caught lying as the crew recorded his live microphone during the conversations.
After this series concluded, a retrospective called Life with Louis was released. Theroux made a documentary called Louis, Martin & Michael about his quest to get an interview with Michael Jackson. Selected episodes of When Louis Met... were included as bonus content on a Best-Of collection of Weird Weekends.
In these special programmes, beginning in 2003, Theroux returned to American themes, working at feature-length and in a more natural way. In March 2006, he signed a new deal with the BBC to make 10 films over the course of three years. Subjects for the specials include criminal gangs in Lagos, Neo-Nazis in America, ultra-Zionists in Israel, where he confirms he is an atheist. He also visits child psychiatry, and the prison systems in California and Florida. A 2007 special, The Most Hated Family in America, received strong critical praise from the international media.
In October 2016, Theroux premiered a feature length documentary entitled My Scientology Movie. Produced by Simon Chinn—a schoolfriend of Theroux's—and directed by John Dower, the film covers Theroux attempting to gain access to the secretive Church of Scientology. The film premiered at the London Film Festival in 2015 and was released in cinemas the UK on 7 October 2016.
Theroux published his first book, The Call of the Weird: Travels in American Subcultures, in Britain in 2005. He recounts his return to the United States to learn about the lives of some of the people he had featured in his television programmes.
As part of the Weird Weekends episode "Porn", Theroux agreed to film a cameo in the 1997 gay pornography film Take a Peak. He did not perform sexual acts in the film, but made a brief appearance as a park ranger in search of a criminal. In the Weird Weekends episode "Infomercials", he was featured as a live salesman for an at-home paper shredder for the Home Shopping Network.
Theroux's first marriage was to Susanna Kleeman; he later told the Financial Times' Sathnam Sanghera, "She was having trouble finding work... legally. So we got married, to make it easier for her. We never really considered ourselves married in the full sense – there were no wedding photos or anything like that. It was really a marriage of convenience."
Theroux later married longtime girlfriend Nancy Strang in 2012. They have three children and live in Harlesden, London. In early 2013, Theroux and his family temporarily moved to Los Angeles, California, allowing him more time to focus on his LA Stories series.
In a 2012 masterclass, Theroux spoke of the challenges of combining family life with the need to go away to work on projects.
Whilst filming for his BBC show America's Most Hated Family in Crisis, he was asked, "Why pose a difference between religion and ethics?" He responded, "Because I don't believe in God." In his documentary The Ultra Zionists, he confirms that he is an atheist.