The Lionhead Studios boss was presented with the accolade by Sir Ben Kingsley, who has previously appeared in Molyneux-created title Fable III.
On receiving the award, Molyneux thanked the entire gaming community and all of his colleagues, before joking that he was "just the idiot that stands up and says, 'Why don't you make a game about theme parks? Or dungeons?'"
He went on to thank the press and admitted that he had been guilty of over-hyping games and inventing new gameplay features in interviews in order to keep journalists awake.
Molyneux finished by thanking his family, before paying tribute to an "incredible" industry.
Mass Effect 2 and Heavy Rain were the other big winners at the 2011 Video Game BAFTAs, which were hosted by comedian Dara O'Briain.
> Click here to see the full list of BAFTA Video Game Awards 2011 winners