Flanagan was born in Longford, Tasmania, in 1961, the fifth of six children. He is descended from Irish convicts transported to Van Diemens Land in the 1840s. His father is a survivor of the Burma Death Railway. One of his three brothers is Australian Rules football journalist Martin Flanagan. He grew up in the remote mining town of Rosebery on Tasmania's western coast.

Flanagan left school at the age of 16. He returned to study at the University of Tasmania, where he was president of the Student Union. He achieved a first class honours degree in 1982. In the following year was awarded a Rhodes Scholarship. At Worcester College, Oxford, he was admitted to the degree of Master of Letters in History.Flanagan wrote four non-fiction works before moving to fiction, works he has called 'his apprenticeship'.

In the foreword to Flanagan's first book, A Terrible Beauty - History of the Gordon River Country (1985), Bob Brown wrote,

Australia has not heard the last of the Tasmanian wilderness nor, I happily predict, has it heard the last of Richard Flanagan.

The first and third novels are set on the West Coast of Tasmania; where he lived in the township of Rosebery as a child. Death of a River Guide relates to the Franklin River, Gould's Book of Fish to the Macquarie Harbour Penal Station, and The Sound of One Hand Clapping to the Hydro settlements in the Central Highlands of Tasmania. He has described these early novels as 'soul histories'. His fourth novel, "The Unknown Terrorist", dedicated to David Hicks, is set in inner Sydney, while his fifth is set in colonial Van Diemen's Land and Victorian London.

The 1998 film of The Sound of One Hand Clapping, directed by Flanagan, was nominated for best film at that year's Berlin Film Festival. Gould's Book of Fish won the 2002 Commonwealth Writers Prize. (When originally published in hardback, it had different sections in different type colour, with plates of the fish paintings interleaved in the text; the paperback edition has them at the rear of the book.)

His novels have won numerous awards and are published in 28 countries.

Flanagan has written on literature, the environment and politics for the Australian and international press. Some has proved controversial. "The Selling-out of Tasmania", published after the death of former Premier Jim Bacon in 2004, was critical of the Bacon government's relationship with corporate interests in the state. Premier Paul Lennon declared, "Richard Flanagan and his fictions are not welcome in the new Tasmania."

Flanagan's 2007 essay, 'Gunns. Out of Control' in The Monthly, first published as 'Paradise Razed' in the London Telegraph, is credited as catalysing Sydney businessman Geoffrey Cousins' high profile campaign against the Gunns' two billion dollar Bell Bay Pulp Mill.

A painting of Richard Flanagan by artist Geoffrey Dyer won the 2003 Archibald Prize.

He worked with Baz Luhrmann as a writer on the film Australia (2008).

Non-Fiction

• (1985) A terrible beauty: history of the Gordon River country
• (1990) The Rest of the world is watching - Tasmania and the Greens
• (1991) Codename Iago: the story of John Friedrich
• (1991) Parish-Fed Bastards. A History of the Politics of the Unemployed in Britain, 1884-1939

Articles

Films

• (1998) The Sound of One hand Clapping" (Director and scriptwriter)
• (2008) Australia (Co-writer)

Novels

• Death of a River Guide (1994)
• The Sound of One Hand Clapping (1997)
• A Novel in Twelve Fish (2001)
• The Unknown Terrorist (2006)
• Wanting (2008)