Lynn was born in Bath, Somerset, to Jewish parents.^[1] He was the son of Robin Lynn, a Scottish physician and Ruth Helen (née Eban), an English sculptor.

His father Robin was from Glasgow, whose own father had come by boat from Lithuania.^[1] His mother Ruth's first cousin on her own mother's side was the neurologist Oliver Sacks;^[2] another cousin, Caroline Sacks, married Nicholas Samuel, 5th Viscount Bearsted.^[3][4][5][6] Lynn's maternal uncle was Israeli statesman Abba Eban,^[1] who, like Jonathan, studied at Cambridge, in the 1930s, and his grandmother was a secretary to Chaim Weizmann, first president of Israel.^[1]

Lynn described his family as "Jewish but secular".^[1] He was teased at school for his Jewishness, but in a later interview shrugged it off, as he believed "They just didn’t know any better".^[1] As a teenager, Lynn played drums in jazz bands.^[1]

Lynn was educated at Kingswood School, Bath, between 1954 and 1961. After he was accepted at age seventeen, he studied law at Pembroke College, Cambridge.^[7] He chose a degree in law despite his love for performing arts, as he said that studying law would "ensure his parents could still sleep at night knowing that their child had a legitimate career to fall back on, just in case".^[7]

While studying at his first year in Cambridge, he met Eric Idle. Idle asked Lynn to join the Cambridge University Footlights Club.^[7] In 1965, he was in the Footlights revue Cambridge Circus. With Bill Oddie, Tim Brooke-Taylor and David Hatch, he appeared on Broadway and on The Ed Sullivan Show.^[8][9][10] Lynn then took acting lessons from actress Mira Rostova.^[7]

Lynn's first West End appearance was in a stage production of Green Julia, for which he was nominated for the 1965 Plays and Players Award as Most Promising New Actor.^[11] In 1967, he played Motel the tailor in the original West End production of Fiddler on the Roof (production recorded by CBS Records).^[12] In 1968, he was in the film Prudence and the Pill. From the late 1960s, Lynn was appearing in and writing television sitcoms, including the television comedy series Twice a Fortnight with Graeme Garden, Bill Oddie, Terry Jones, Michael Palin and Tony Buffery.^[13]

Lynn played the Irish medical student Danny Hooley in the second series of the television comedy Doctor in the House in 1970, replacing Martin Shaw, who played Welsh man Huw Evans. He wrote some episodes for future series in the Doctor in the House franchises including Doctor at Large, Doctor in Charge, Doctor at Sea and Doctor on the Go.^[6][14] He also wrote episodes of On the Buses and wrote for Harry Worth and George Layton. In the 1970s, his most memorable roles included Beryl's boyfriend Robert in early series of The Liver Birds;^[15] Harold in Jack Rosenthal's 1976 television film Bar Mitzvah Boy,;^[16] and Ted Margolis in Rosenthal's The Knowledge (1979).^[17]

His film appearances included roles in The House That Dripped Blood (1971), and Romance with a Double Bass (1974) He had a bit-part as a window cleaner in the BBC television series The Good Life. Lynn's first (co-written) screenplay was for The Internecine Project, which was released in 1974.^[18]

After forming a partnership with Antony Jay, they would begin working with one another, eventually writing Yes Minister, which aired from 1980 to 1988.^[19] His directoral debut came in 1985, with Clue.^[20]

On 20 October 1984, he was the subject of an episode of the radio series Desert Island Discs, in which he picked a collection of Jeeves & Wooster novels by P G Wodehouse as his book of choice, a pen and paper as his luxury items, and songs written and/or composed by Wolfgang Amadeus Mozart, Ludwig van Beethoven, Jimmy Durante and Paul Simon.^[21][22]

Lynn co-authored the books The Complete Yes Minister, as well as The Complete Yes Prime Minister, which spent 106 weeks on the Sunday Times top 10 fiction list. Both were ranked number one on the Sunday Times list, including in December 1986 when the books were ranked number one and number two respectively.^[23] He also wrote the 1993 novel Mayday.^[24]

In the 1990s, Lynn directed some of his most well-known films, including Nuns on the Run (1990), My Cousin Vinny (1992), The Distinguished Gentleman (1992), Greedy (1994), Sgt. Bilko (1996), and Trial and Error (1997). Lynn also served as a producer for Trial and Error,^[9] which received an exclusive production agreement with Columbia Pictures Television in 1992.^[25] Lynn's last acting credit came in 1994 when he appeared as a butler in Greedy.^[26]

He was executive producer of Vanity Fair in 2004, and He's Such a Girl in 2008.

Lynn won praise for his direction of the 2010 London stage version of Yes, Prime Minister, which he co-wrote as well.^[27]

In 2011 Lynn wrote a non-fiction work entitled Comedy Rules. The Independent called the book "a charming memoir, full of amusing and insightful anecdotes about the many entertainers Lynn has worked with" and described it as a combination of autobiography and how-to manual for comedy. The paper wrote further: "By dovetailing different types of book, Lynn cleverly avoids the pitfalls of both genres. Because it's ostensibly a sort of how-to book, there are no boring childhood reminiscences. Because it's also a kind of autobiography, his no-nonsense dos and don'ts are springboards for entertaining yarns, rather than academic discourse."^[28]

Lynn co-wrote, co-produced, and co-directed the Yes, Minister revival series Yes, Prime Minister series produced by the BBC on Gold in 2013.^[29]

In 2016 Lynn's play The Patriotic Traitor was published. Its subject is the relationship of Philippe Pétain to Charles de Gaulle. In the words of the blurb, ‘Two giants of the twentieth century who loved each other like father and son until they found themselves on opposing sides in World War II. In 1945 de Gaulle had his oldest friend tried for treason. Their complex relationship – noble, comic and absurd – changed history.’ ^[30][31]

Lynn also co-wrote the stage play of "Clue", together with Hunter Foster, Eric Price and Sandy Rustin.

Lynn has been married to his wife, Canadian-born actress Rita Markelis, since 1 August 1967.

Lynn has lived in America for many years, primarily living in New York,^[32] and has acquired U.S. citizenship.^[1] In 2020, he and his wife put up their condo apartment on 54th Street in Manhattan for sale for $2.89 million.^[33]

He is a guest instructor at New York's HB Studio.^[34]

In 2018, Lynn criticized statements made by Jeremy Corbyn after Corbyn had attended a speech given in Parliament by Palestinian academic Manuel Hassassian. Corbyn claimed that after speaking, Hassassian was berated by certain Zionists in the audience, who Corbyn said had failed to understand the "English irony" employed in Hassassian's rhetoric. Lynn, in a letter to The Times, wrote "I am Jewish. Although I wrote Yes Minister and Yes, Prime Minister, Corbyn says I don’t understand English irony. My co-writer Tony Jay was only half-Jewish, so perhaps he half-understood irony and was able to supply some".^[35][36][37]

Lynn's work on the Minister series earned him three BAFTAs, two Broadcasting Press Guild Awards, and two Pye Television Writers Awards, and he won the ACE Award for Best Written Comedy Series. The Campaign for Freedom of Information also recognized Lynn with a special award for his work on the show.^[9] Lynn was a recipient of a Diamond Jubilee Award for Political Satire in 2010.^[38] He received an NAACP Image Award for the 2003 film The Fighting Temptations.^[39]

• Cambridge Arts Theatre