Flanagan was awarded the 50,000 pound ($A96,000) Baillie Gifford Prize on Tuesday for his genre-bending memoir Question 7, which combines autobiography, family history and the story of the development of the atomic bomb.
Flanagan won the Booker Prize in 2014 for The Narrow Road To The Deep North, a novel that drew on his father's experiences as a World War II prisoner of the Japanese military.
Baillie Gifford Prize director Toby Mundy said that for the same writer to win the leading UK-based fiction and nonfiction awards was "completely unprecedented".
Journalist Isabel Hilton, who chaired the judging panel, said Flanagan had written a "meditative symphony of a book" that weaves together "enormous traumatic events of the 20th century … with an extraordinary personal narrative."
Hilton said Flanagan's fiction background was evident in the book's inventiveness and "narrative beat."
"... The book benefited from that novelist's eye," she said.
Flanagan was not on hand to receive the trophy in person at a ceremony in London. Organisers said he was trekking in the Tasmanian rainforest.
Flanagan's book beat five other finalists, including American writer Annie Jacobsen's sobering Nuclear War: A Scenario, and Pulitzer Prize-winner Viet Thanh Nguyen's autobiographical A Man Of Two Faces: A Memoir, A History, A Memorial.
Founded in 1999, the Baillie Gifford Prize recognises English-language books in current affairs, history, politics, science, sport, travel, biography, autobiography and the arts. It has been credited with bringing an eclectic slate of fact-based books to a wider audience.
