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The Oscar-winning director, whose films include Shallow Grave, Trainspotting and Slumdog Millionaire, closes this year's event with his latest movie 127 Hours.
Boyle will be given the honour at a ceremony on October 27 at Jerwood Hall, LSO St Luke's, where the other prize-winners from this year's festival will also be announced.
"A significant helping of humility is called for in the face of this honour and that is not difficult considering those awarded it before," Boyle said.
"I am shocked, flattered and delighted to receive the Fellowship on behalf of everyone who has helped me make the films, the successful ones and the not so successful ones, and on behalf of all runts in every litter."
Other stars previously named as BFI Fellows include Clint Eastwood, Graham Greene, Sir Alec Guinness, Sir David Lean, Mike Leigh, Ken Loach, Martin Scorsese, Ridley Scott and Orson Welles.
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