The honour is the highest accolade handed out by BAFTA for outstanding and exceptional contribution to film. Previous recipients of the award include Alfred Hitchcock, Steven Spielberg, Sean Connery, Judi Dench, Vanessa Redgrave, Christopher Lee and Martin Scorsese.
"When you make your first film, you're sure it will be your last," Parker said. "And then you squeeze your eyes together and suddenly, 40 years later, you're at BAFTA getting an award like this. I'm of course enormously flattered and honoured."
BAFTA chairman John Willis added: "Sir Alan Parker is a hugely distinctive filmmaker, and a man of uncompromising vision and personality. He has made an immense contribution to the British film industry, receiving a wide range of critical and public acclaim for his writing, producing and directing across almost 40 years of filmmaking.
[Madonna in Alan Parker's 'Evita']
"It's almost impossible to highlight any one moment of his career, but the incredible 19 BAFTAs his films have won indicate the esteem in which he is held by his peers, as well as the outstanding nature of his work. I'm delighted that the Academy has taken this opportunity to recognise Sir Alan with the Fellowship this year."
Parker began his career as a copywriter and director of TV adverts, before making his film directorial debut with Bugsy Malone in 1976.
His other films include Midnight Express, Fame, Pink Floyd The Wall and The Commitments. His most recent film, the Kevin Spacey-led Life of David Gale, was released in 2003.
The EE BAFTAs, hosted by Stephen Fry, will take place on Sunday, February 10 from London's Royal Opera House.
EE BAFTA Film Awards - 2013 nominations in pictures - photo gallery: