Cleese was born in Weston-super-Mare, Somerset, the only child of Reginald Francis Cleese (1893–1972), an insurance salesman, and his wife Muriel Evelyn (née Cross; 1899–2000). His family's surname was originally Cheese, but his father had thought it was embarrassing and changed it when he enlisted in the Army during the First World War. As a child, Cleese supported Bristol City FC and Somerset County Cricket Club. Cleese was educated at St Peter's Preparatory School, where he received a prize for English and did well at cricket and boxing. When he was 13, he was awarded an exhibition at Clifton College, an English public school in Bristol. He was already more than 6 feet (1.83 m) tall by then.

At the Footlights theatrical club, he spent a lot of time with Tim Brooke-Taylor and Bill Oddie and met his Future writing partner Graham Chapman. Cleese wrote extra material for the 1961 Footlights Revue I Thought I Saw It Move, and was Registrar for the Footlights Club during 1962. He was also in the cast of the 1962 Footlights Revue Double Take! Cleese graduated from Cambridge in 1963 with a 2:1. Despite his successes on The Frost Report, his father would send him cuttings from The Daily Telegraph offering management jobs in places like Marks and Spencer.

Cleese was a scriptwriter, as well as a cast member, for the 1963 Footlights Revue A Clump of Plinths. The revue was so successful at the Edinburgh Festival Fringe that it was renamed Cambridge Circus and taken to the West End in London and then on a tour of New Zealand and Broadway, with the cast also appearing in some of the revue's sketches on The Ed Sullivan Show in October 1964.

Also in 1965, Cleese and Chapman began writing on The Frost Report. The writing staff chosen for The Frost Report consisted of a number of Writers and performers who would go on to make names for themselves in comedy. They included co-performers from I'm Sorry, I'll Read That Again and Future Goodies Bill Oddie and Tim Brooke-Taylor, and also Frank Muir, Barry Cryer, Marty Feldman, Ronnie Barker, Ronnie Corbett, Dick Vosburgh and Future Python members Eric Idle, Terry Jones, and Michael Palin. While working on The Frost Report, the Future Pythons developed the writing styles that would make their collaboration significant. Cleese's and Chapman's sketches often involved authority figures, some of whom were performed by Cleese, while Jones and Palin were both infatuated with filmed scenes that opened with idyllic countryside panoramas. Idle was one of those charged with writing David Frost's monologue. During this period Cleese met and befriended influential British Comedian Peter Cook.

It was as a performer on The Frost Report that Cleese achieved his breakthrough on British television as a comedy actor, appearing as the tall, patrician figure in the classic class Sketch, contrasting comically in a line-up with the shorter, middle class Ronnie Barker and the even shorter, working class Ronnie Corbett. This series was so popular that in 1966 Cleese and Chapman were invited to work as Writers and performers with Brooke-Taylor and Feldman on At Last the 1948 Show, during which time the Four Yorkshiremen Sketch was written by all four writers/performers (the Four Yorkshiremen Sketch is now better known as a Monty Python sketch). Cleese and Chapman also wrote episodes for the first series of Doctor in the House (and later Cleese wrote six episodes of Doctor at Large on his own in 1971). These series were successful, and in 1969 Cleese and Chapman were offered their very own series. However, owing to Chapman's alcoholism, Cleese found himself bearing an increasing workload in the partnership and was, therefore, unenthusiastic about doing a series with just the two of them. He had found working with Palin on The Frost Report an enjoyable experience and invited him to join the series. Palin had previously been working on Do Not Adjust Your Set with Idle and Jones, with Terry Gilliam creating the animations. The four of them had, on the back of the success of Do Not Adjust Your Set, been offered a series for Thames Television, which they were waiting to begin when Cleese's offer arrived. Palin agreed to work with Cleese and Chapman in the meantime, bringing with him Gilliam, Jones, and Idle.

Cleese met Connie Booth in the US and they married in 1968. In 1971, Booth gave birth to Cynthia Cleese, their only child. With Booth, Cleese wrote the scripts for and co-starred in both series of Fawlty Towers, even though the two were actually divorced before the second series was finished and aired. Cleese and Booth are said to have remained close friends since. Cleese has two grandchildren, Evan and Olivia, through his eldest daughter's marriage to Ed Solomon.

Monty Python's Flying Circus ran for four seasons from October 1969 to December 1974 on BBC Television, though Cleese quit the show after the third. Cleese's two primary characterisations were as a sophisticated and a stressed-out loony. He portrayed the former as a series of announcers, TV show hosts, and government officials (for Example, "The Ministry of Silly Walks"). The latter is perhaps best represented in the "Cheese Shop" and by Cleese's Mr Praline character, the man with a dead Norwegian Blue parrot and a menagerie of other animals all named "Eric". He was also known for his working class "Sergeant Major" character, who worked as a Police Sergeant, Roman Centurion, etc. He is also seen as the opening announcer with the now famous line "And now for something completely different", although in its premiere in the Sketch "Man with Three Buttocks", the phrase was spoken by Eric Idle.

From 1970 to 1973, Cleese served as rector of the University of St Andrews. His election proved a milestone for the university, revolutionising and modernising the post. For instance, the rector was traditionally entitled to appoint an "Assessor", a deputy to sit in his place at important meetings in his absence. Cleese changed this into a position for a student, elected across campus by the student body, resulting in direct access and representation for the student body.

The first series was screened from 19 September 1975 on BBC 2, initially to poor reviews, but gained momentum when repeated on BBC 1 the following year. Despite this, a second series did not air until 1979, by which time Cleese's marriage to Booth had ended, but they revived their collaboration for the second series. Fawlty Towers consisted of only twelve episodes; Cleese and Booth both maintain that this was to avoid compromising the quality of the series.

Around this time, Cleese worked with Comedian Les Dawson on his sketch/stand-up show Sez Les. The differences between the two physically (the tall, lean Cleese and the short, stout Dawson) and socially (the public school, and then Cambridge-educated Cleese and the working class, self-educated Mancunian Dawson) were marked, but both worked well together from series 8 onwards until the series ended in 1976.

In December 1977, Cleese appeared as a guest star on The Muppet Show. Cleese was a fan of the show and co-wrote much of the episode. Cleese also made a cameo appearance in their 1981 film The Great Muppet Caper.

During the 1980s and 1990s, Cleese focused on film, though he did work with Peter Cook in his one-off TV special Peter Cook and Co. in 1980. In the same year, Cleese played Petruchio, in Shakespeare's The Taming of the Shrew in the BBC Television Shakespeare series. In 1981 he starred with Sean Connery and Michael Palin in the Terry Gilliam-directed Time Bandits as Robin Hood. He also participated in Monty Python Live at the Hollywood Bowl (1982) and starred in The Secret Policeman's Ball for Amnesty International. In 1985, Cleese had a small dramatic role as a sheriff in Silverado, which had an all-star cast that included Kevin Kline, with whom he would star in A Fish Called Wanda three years later. In 1986, he starred in Clockwise as an uptight school headmaster obsessed with punctuality and constantly getting into trouble during a journey to speak at the Headmasters' Conference.

Cleese married American Actress Barbara Trentham in 1981. Their daughter Camilla, Cleese's second child, was born in 1984. He and Trentham divorced in 1990. During this time, Cleese moved to Los Angeles.

Timed with the 1987 UK elections, he appeared in a video promoting proportional representation.

In 1988, he wrote and starred in A Fish Called Wanda as the lead, Archie Leach, along with Jamie Lee Curtis, Kevin Kline, and Michael Palin. Wanda was a commercial and critical success, and Cleese was nominated for an Academy Award for his script. Cynthia Cleese starred as Leach's daughter.

Graham Chapman was diagnosed with throat cancer in 1989; Cleese, Michael Palin, Peter Cook, and Chapman's partner David Sherlock, witnessed Chapman's death. Chapman's death occurred a day before the 20th anniversary of the first broadcast of Flying Circus, with Jones commenting, "the worst case of party-pooping in all history." Cleese's eulogy at Chapman's memorial service—in which he "became the first person ever at a British memorial Service to say 'fuck'"—has since become legendary.

In 1992, he married American psychotherapist Alyce Faye Eichelberger. They divorced in 2008. The divorce settlement left Eichelberger with £12 million in Finance and assets, including £600,000 a year for seven years. Cleese said, "What I find so unfair is that if we both died today, her children would get much more than mine ... I got off lightly. Think what I'd have had to pay Alyce if she had contributed anything to the relationship – such as children, or a conversation."

In 1996, Cleese declined the British honour of Commander of the Order of the British Empire (CBE). The follow-up to A Fish Called Wanda, Fierce Creatures—which again starred Cleese alongside Kevin Kline, Jamie Lee Curtis, and Michael Palin—was also released that year, but was greeted with mixed reception by critics and audiences. Cleese has since often stated that making the second film had been a mistake. When asked by his friend, Director and restaurant critic Michael Winner, what he would do differently if he could live his life again, Cleese responded, "I wouldn't have married Alyce Faye Eichelberger and I wouldn't have made Fierce Creatures."

Cleese has a passion for lemurs. Following the 1997 comedy film Fierce Creatures, in which the ring-tailed lemur played a key role, he hosted the 1998 BBC documentary In the Wild: Operation Lemur with John Cleese, which tracked the progress of a reintroduction of black-and-white ruffed lemurs back into the Betampona Reserve in Madagascar. The project had been partly funded by Cleese's donation of the proceeds from the London premier of Fierce Creatures. Cleese is quoted as saying, "I adore lemurs. They're extremely gentle, well-mannered, pretty and yet great fun ... I should have married one."

Cleese is Provost's Visiting Professor at Cornell University, after having been Andrew D. White Professor-at-Large from 1999 to 2006. He makes occasional well-received appearances on the Cornell campus.

Cleese achieved greater prominence in the United Kingdom as the neurotic hotel manager Basil Fawlty in Fawlty Towers, which he co-wrote with his wife Connie Booth. The series won three BAFTA awards when produced and in 2000, it topped the British Film Institute's list of the 100 Greatest British Television Programmes. The series also featured Prunella Scales as Basil's acerbic wife Sybil, Andrew Sachs as the much abused Spanish waiter Manuel ("... he's from Barcelona"), and Booth as waitress Polly, the series' voice of sanity. Cleese based Basil Fawlty on a real person, Donald Sinclair, whom he had encountered in 1970 while the Monty Python team were staying at the Gleneagles Hotel in Torquay while filming inserts for their television series. Reportedly, Cleese was inspired by Sinclair's mantra, "I could run this hotel just fine if it weren't for the guests." He later described Sinclair as "the most wonderfully rude man I have ever met," although Sinclair's widow has said her husband was totally misrepresented in the series. During the Pythons' stay, Sinclair allegedly threw Idle's briefcase out of the hotel "in case it contained a bomb," complained about Gilliam's "American" table manners, and threw a bus timetable at another guest after they dared to ask the time of the next bus to town.

In 2001, Cleese was cast in the comedy Rat Race as the eccentric hotel owner Donald P. Sinclair, the name of the Torquay hotel owner on whom he had based the character of Basil Fawlty. In 2002, Cleese made a cameo appearance in the film The Adventures of Pluto Nash in which he played "James", a computerised chauffeur of a hover car stolen by the title character (played by Eddie Murphy). The vehicle is subsequently destroyed in a chase, leaving the chauffeur stranded in a remote place on the moon. In 2003, Cleese appeared as Lyle Finster on the US sitcom Will & Grace. His character's daughter, Lorraine, was played by Minnie Driver. In the series, Lyle Finster briefly marries Karen Walker (Megan Mullally). In 2004, Cleese was credited as co-writer of a DC Comics graphic novel titled Superman: True Brit. Part of DC's "Elseworlds" line of imaginary stories, True Brit, mostly written by Kim Howard Johnson, suggests what might have happened had Superman's rocket ship landed in Britain, not America.

The Bemaraha woolly lemur (Avahi cleesei), also known as Cleese's woolly lemur, is native to western Madagascar. The scientist who discovered the species named it after Cleese, mainly because of Cleese's fondness for lemurs and his efforts at protecting and preserving them. The species was first discovered in 1990 by a team of Scientists from Zurich University led by Urs Thalmann, but was not formally described as a species until 11 November 2005.

In 2007, Cleese appeared in ads for Titleist as a golf course designer named "Ian MacCallister", who represents "Golf Designers Against Distance". Also in 2007, he started filming the sequel to The Pink Panther, titled The Pink Panther 2, with Steve Martin and Aishwarya Rai. On 27 September 2007, Cleese announced he was to produce a series of video podcasts called HEADCAST. Cleese released the first episode of this series in April 2008 on his own website, headcast.co.uk.

In 2008, Cleese expressed support for Barack Obama and his presidential candidacy, offering his services as a speech Writer. He was an outspoken critic of Republican Vice-Presidential candidate Sarah Palin, saying that "Michael Palin is no longer the funniest Palin". The same year, he wrote a satirical poem about Fox News commentator Sean Hannity for Countdown with Keith Olbermann.

In 2009 and 2010, Cleese toured Scandinavia and the US with his Alimony Tour Year One and Year Two. In May 2010, it was announced that this tour would extend to the UK (his first tour in the UK), set for May 2011. The show is dubbed the "Alimony Tour" in reference to the financial implications of Cleese's divorce. The UK tour started in Cambridge on 3 May, visiting Birmingham, Nottingham, Salford, York, Liverpool, Leeds, Glasgow, Edinburgh, Oxford, Bristol and Bath (the Alimony Tour DVD was recorded on 2 July, the final Bath date). Later in 2011 John took his Alimony Tour to South Africa. He played Cape Town on the 21 & 22 October before moving over to Johannesburg where he played from 25 to 30 October. In January 2012 he took his one-man show to Australia, starting in Perth on 22 Jan and throughout the next 4 months visited Adelaide, Brisbane, Gold Coast, Newcastle, New South Wales, Melbourne, Sydney, and finished up during April in Canberra.

In October 2010, Cleese was featured in the launch of an advertising campaign by The Automobile Association for a new home emergency response product. He appeared as a man who believed the AA could not help him during a series of disasters, including water pouring through his ceiling, with the line "The AA? For faulty showers?" During 2010, Cleese appeared in a series of radio advertisements for the Canadian insurance company Pacific Blue Cross, in which he plays a character called "Dr. Nigel Bilkington, Chief of Medicine for American General Hospital".

In April 2011, Cleese revealed that he had declined a life peerage for political services in 1999. Outgoing leader of the Liberal Democrats, Paddy Ashdown, had put forward the suggestion shortly before he stepped down, with the idea that Cleese would take the party whip and sit as a working peer, but the actor quipped that he "realised this involved being in England in the winter and I thought that was too much of a price to pay."

In August 2012, Cleese married English jewellery designer and former model Jennifer Wade in a ceremony in the Caribbean.

At a comic press conference in November 2013, Cleese and other surviving members of the Monty Python comedy group announced a reuniting performance to be held in July 2014.

In an interview with The Daily Telegraph in 2014, Cleese expressed political interest with regard to the UK Independence Party, saying that although he was in doubt as to whether he was prepared to vote for them, he was attracted to its challenge to the established political order and the radicalism of its policies with regard to the United Kingdom's membership of the European Union. He expressed support for immigration but also concern about the integration of immigrants into British culture.

In March 2015, in an interview with Der Spiegel, he was asked if he was religious. Cleese stated that he didn't think much of organised religion and said he was not committed to "anything except the vague feeling that there is something more going on than the materialist reductionist people think".

During then-Republican nominee Donald Trump's run for the US Presidency in 2016, Cleese described Trump as "a narcissist, with no attention span, who doesn't have clear ideas about anything and makes it all up as he goes along". He had previously described the leadership of the Republican Party as "the most cynical, most disgracefully immoral people I've ever come across in a Western civilisation".