This is her second book in her Thomas Cromwell trilogy.
"You wait 20 years for a Booker Prize; two come along at once," said Mantel upon accepting the award.
Mantel had won the Booker in 2009 for her book 'Wolf Hall', which makes her the first British writer to win the Man Booker Prize twice.
The 60-year-old writer said that she regarded the award as an "act of faith and a vote of confidence".
Hilary Mantel received a £50,000 prize, in addition to the £2,500 awarded to all six shortlisted writers.
The judging panel included Times Literary Supplement editor Peter Stothard and "Downton Abbey" actor Dan Stevens. The award was announced during a dinner ceremony at London's medieval Guildhall.
Indian author Jeet Thayil's debut novel on the dark underside of Mumbai's opium dens was in race for this year's prestigious Man Booker prize.
The award, established in 1969, is open to writers from Britain, Ireland and the Commonwealth of former British colonies.
Jeet Thayil on Man Booker shortlist
Will Jeet Thayil be the fifth Indian to claim Booker?