The annual award is Bafta’s highest accolade and was bestowed to actor Christopher Lee last year.
Bafta chair Tim Corrie called Scorsese “a legend in his lifetime, a true inspiration to all young directors”.
The film-maker will collect his accolade at the Bafta Awards in London on 12 February.
Scorsese, whose latest movie Hugo has been applauded by the critics, said: “It is a great honour to be recognized by the British Academy and to join the ranks of such an esteemed group of industry colleagues and friends.”
Previous recipients from the discipline of film-making to gain the award include Steven Spielberg, Alfred Hitchcock and Stanley Kubrick.
Scorsese’s film career spans six decades, with work including Taxi Driver, Gangs of New York and The Aviator.
He has picked up nine Bafta nominations for directing, winning in 1991 for Goodfellas.
The film-maker, 69, picked up a string of Oscar nods during a long wait to finally win best director for The Departed in 2007.
In 1990,he founded The Film Foundation, a nonprofit organization dedicated to film preservation.
Previous honorary accolades for his life’s work have included a Cesar in France, a life achievement from the American Film Institute in 1997 and recognition from the Director’s Guild of America in 2003.
Scorsese’s most recent film Hugo marks his first foray into 3D movie-making in the family film genre.