The Taxi Driver and Raging Bull legend will be presented with the Academy's highest accolade in recognition of his contribution to the film industry - and the 69 year old is thrilled with the award.
He says, "It is a great honour to be recognised by the British Academy and to join the ranks of such an esteemed group of industry colleagues and friends."
BAFTA boss Tim Corrie adds, "Martin Scorsese is a legend in his lifetime - a true inspiration to all young directors the world over. We are delighted to honour his contribution to cinema history and look forward to paying tribute to him in London on 12 February."
Previous winners include Charlie Chaplin, Alfred Hitchcock, Steven Spielberg, Dame Elizabeth Taylor, Sir Anthony Hopkins, Dame Judi Dench and Vanessa Redgrave. Sir Christopher Lee was presented with a Fellowship at last year's event.
The BAFTA awards will take place in London on 12 February.