The Fable creator will be the fourth person to receive the Fellowship after Shigeru Miyamoto, Nolan Bushnell and Will Wright.
"I remember back in 1967 watching the first BAFTA awards on television with my family and seeing them being so excited about those accolades," said Molyneux.
"Never in my wildest dreams did I ever think it would be possible for me to accept one of the greatest honours the entertainment industry has to offer.
"My first thought on learning that I was awarded an Academy Fellowship was that to be in the company of some of the greatest talents the entertainment industry has ever seen is truly humbling, and secondly that this is an award not just for myself, but for all the people I've ever worked with."
BAFTA chief executive Amanda Berry OBE added: "We are delighted to be honouring Peter at this point in his long and successful career in video games.
"He is one of the leading figures in the development of video games as an art form and an inspiration to the next generation of creative minds."
Peter Molyneux co-founded Bullfrog Productions in 1987 and helped create the God-simulation genre, releasing titles such as Populous, Powermonger, Theme Park and Magic Carpet.
The awards, which has seen Assassin's Creed Brotherhood nominated for seven prizes, will take place on March 16.