The director was given the accolade by BFI Chair Greg Dyke after a screening of his film Robin and Marian at the BFI Southbank.
Lester said: "When my career was just beginning, the elegant TV critic Bernard Levin came to see me in rehearsal with Spike Milligan and Peter Sellers.
"He wrote, 'He seems an amiable young man who climbed into a lion's cage and realised he's forgotten his chair and his whip'.
"Some 50 years later, I still haven't found a whip, but with this extraordinary honour, the BFI has kindly given me a chair."
Dyke added: "Richard Lester has created a unique body of work which has enriched the lives of millions with his brilliantly surreal humour and innovative style.
"Although born in America he has lived in Britain for 60 years and created some of the most enduring and influential creations of British cinema."
Born in 1932, Lester came to England in 1956 and has remained a resident since.
After he and Sellers directed the Oscar-nominated short The Running Jumping & Standing Still Film Lester was chosen to direct The Beatles' first two films A Hard Day's Night (1964) and Help! (1965).
Past recipients of the BFI Fellowship have included Danny Boyle, Ralph Fiennes, Martin Scorsese, Judi Dench and David Cronenberg.
Watch Richard Lester's The Running Jumping and Standing Still Film below: