Sir Kenneth Branagh presented the Queen with the award in a star-studded gala at Windsor Castle.
BAFTA chairman John Willis described Queen Elizabeth as “the most memorable Bond girl yet” – a reference to her cameo in the London Olympics opening ceremony.
Hollywood director George Lucas, who flew in especially for the event, said the UK had been influential for him.
John Willis said: “We should be proud of our industry. The people here this evening represent a vast variety of skills and ground breaking innovation, they have entertained and informed a generation and inspired generations to come.
“I am delighted that this evening has given us the opportunity to give something back. I have the great honor to announce that we are to present Her Majesty with an honorary BAFTA today, in recognition of her outstanding patronage of the film and television industries.”
The Queen, who attended with Prince Philip, featured with Daniel Craig as James Bond at London 2012 – when she appeared to parachute from a helicopter.
To laughter from the audience, actor Kenneth Branagh said: “Your sensational appearance at the opening ceremony of last year’s Olympics was especially memorable.
“So much so that several of my colleagues here tonight want you to know that should you wish to take it further into the world of British films that they have a number of scripts with them here this evening. I have to warn you, Your Majesty, not all of these films are fully financed.”
The 300 guests represented all areas of the industry including actors, directors, writers, producers, costume and set designers, publicists and critics.
Homeland star Damian Lewis, who attended the event with his actress wife Helen McCrory, said: “The arts and film industry punch above their weight with little funding.
“Our arts in this country and theatre and film and TV are some of our greatest exports, to have that recognized by your monarch is important.”
Comedian Billy Connolly attended the reception as did director Terry Gilliam, actress Minnie Driver and actor Idris Elba.
Actor John Hurt also commented on the Queen’s appearance at the Olympics.
“It was a bit of good fun, I thought so – good on her,” he said.
John Hurt revealed he had come to the event from filming Doctor Who, for its 50th anniversary, in Cardiff.
George Lucas said: “I’ve been here since ’75 so for me this is my second home.
“It’s been very influential for me, I’ve shot lots of movies here not only four of the Star Wars films but also Indiana Jones, all kinds of films – it’s been a long road.”
He added: “Many, many years ago Britain didn’t support the film industry and when I came here it was on its last legs and fortunately now it’s a lot steadier.”
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