Haddon was born in 1962 in Northampton and educated at Uppingham School and Merton College, Oxford, where he studied English.

In 2003, Haddon won the Whitbread Book of the Year Award and in 2004, the Commonwealth Writers' Prize Overall Best First Book for his novel The Curious Incident of the Dog in the Night-time, a book which is written from the perspective of a boy with Asperger syndrome. However, Haddon has stated on his website that he knows "very little about the subject", and that he "slightly regret[s]" that the term "Asperger syndrome" appeared on the cover of his book. Moreover, he had done no research about autism before writing the novel. Rather, he recommends that one read works by people who have Asperger syndrome themselves. In an interview at Powells.com, Haddon claimed that this was the first book that he wrote intentionally for an adult audience; he was surprised when his publisher suggested marketing it to both adult and child audiences. His second adult novel, A Spot of Bother, was published in September 2006.

Mark Haddon is also known for his series of Agent Z books, one of which, Agent Z and the Penguin from Mars, was made into a 1996 Children's BBC sitcom. He also wrote the screenplay for the BBC television adaptation of Raymond Briggs's story Fungus the Bogeyman, screened on BBC1 in 2004. In 2007 he wrote the BBC television drama Coming Down the Mountain.

Haddon is a vegetarian, and enjoys vegetarian cookery. He describes himself as a 'hard-line atheist'. In an interview with The Observer, Haddon said "I am atheist in a very religious mould". His atheism might be inferred from The Curious Incident of the Dog in the Night-time in which the main character declares that those who believe in God are stupid.

In 2009, he donated the short story The Island to Oxfam's 'Ox-Tales' project, four collections of UK stories written by 38 authors. Haddon's story was published in the 'Fire' collection.

Mark Haddon lives in Oxford with his wife Dr. Sos Eltis, a Fellow of Brasenose College, Oxford, and their two young sons.

Youth titles

• Gilbert's Gobstopper (1987)
• Mikie Joy
• Toni and the Tomato Soup (1988)
• A Narrow Escape for Princess Sharon (1989)
• Agent Z Meets the Masked Crusader (1993)
• Titch Johnson, Almost World Champion (1993)
• Agent Z Goes Wild (1994)
• At Home
• At Playgroup
• In the Garden
• On Holiday
• Gridzbi Spudvetch! (1992)
• The Real Porky Phillips (1994)
• Agent Z and the Penguin from Mars (1995)
• The Sea of Tranquility (1996)
• Secret Agent Handbook
• Agent Z and the Killer Bananas (2001)
• Ocean Star Express (2001)
• The Ice Bear's Cave (2002)
• Boom! (2009)

For adults

• The Curious Incident of the Dog in the Night-time (2003)
• A Spot of Bother (2006)

Poetry

• The Talking Horse and the Sad Girl and the Village Under the Sea