Birkin left Harrow School at the age of 17 to work as a mail boy at 20th Century Fox’s London office, graduating to Elstree Studios as a production runner in 1963. He began work as a runner on Stanley Kubrick’s A Space Odyssey in 1965, but soon became Kubrick's location scout. By the summer of 1966, Kubrick had promoted Birkin to Assistant Director on Special Effects; Birkin later proposed the shooting and color transposition of aerial footage for the 'Jupiter and Beyond the Infinite' sequence, some of which he filmed from a helicopter over Scotland. In 1967 Birkin supervised the shooting of 'The Dawn of Man' front projection plates in the Namib Desert. In 1968, Kubrick again engaged Birkin as his assistant director and location scout on his unmade epic of Napoleon.

After working as First Assistant Director to The Beatles on Magical Mystery Tour in 1967, Birkin began writing scripts for producer David Puttnam, including The Pied Piper (1971) for director Jacques Demy, Slade In Flame (1974) for the rock band Slade (which won the Vision Award at the 2007 MOJO Awards), and an unmade adaptation of Albert Speer's Inside the Third Reich for Puttnam and Paramount, which involved a year’s collaboration and taped interviews with Speer in 1972.

Having worked on an adaptation of Peter Pan for NBC in 1975, Birkin conceived and wrote The Lost Boys (1978), a 3-part mini-series for the BBC about Peter Pan's creator J. M. Barrie, which won him writing awards from the Writers Guild of Great Britain and The Royal Television Society. The critic Sean Day-Lewis wrote in The Daily Telegraph, 'I doubt if biography has ever been better televised than in this sensitive and beautifully crafted masterpiece, and I am quite sure such excellence is beyond any other television service in the world.' The BBC's Director-General Sir Ian Trethowan called it 'a landmark in television drama'. Birkin has also written a biographical account of Barrie's relationship with the Llewelyn Davies family, J. M. Barrie and the Lost Boys (1979; 2nd edition 2003), described by The Oxford Companion to Children's Literature as 'the most candid and perceptive biography to have been written of Barrie'. Birkin also hosts Barrie's official website on behalf of the Great Ormond Street Hospital, to whom he donated his Barrie/Llewelyn Davies/Peter Pan archive in 2004.

In 1980, Birkin won a BAFTA award and an Academy Award nomination for his short film Sredni Vashtar, based on the short story by Saki, which he wrote, produced and directed for 20th Century Fox. In 1984 he wrote the shooting script for The Name of the Rose (in which he also had a small acting role), and in 1988 he wrote and directed Burning Secret, based on the novel by Stefan Zweig, which won two awards at the 1989 Venice Film Festival, as well as the Young Jury prize for Best Film at the Brussels Film Festival. In 1993, Birkin wrote and directed The Cement Garden, based on the novel by Ian McEwan, for which he won the Silver Bear as best director at the Berlin Film Festival, as well as Best Film at several film festivals, including Dinard, Fort Lauderdale, and Birmingham. In 1998 he collaborated with Luc Besson on the script of The Story of Joan of Arc, and in 2004 co-wrote the screenplay for The Story of a Murderer.

In 2009 Birkin wrote a screenplay for Heathcliff Films based on Mark Kurzem's The Mascot. He is currently adapting Julia Stuart's The Matchmaker of Périgord for Ratpack Films, as well as writing/directing Vernon God Little for Bernd Eichinger and Constantin Film.

Birkin has three sons: David Birkin (born 1977), artist and photographer; Anno Birkin (born 1980), poet and musician, who was killed in 2001; and Ned Birkin (born 1985), whom Birkin directed in The Cement Garden and with whom he is currently writing a television docudrama. Two of his nieces are actresses: Charlotte Gainsbourg, who also appeared in The Cement Garden, and Lou Doillon. He is married to artist Karen Birkin, with whom he has a daughter, Emily Jane (born December 2008). He lives on the Ll?n Peninsula in North Wales.