The Minecraft developer will be presented with the accolade for his creative contribution to the games industry.
"I've always considered the BAFTA Awards to be one of the most prestigious awards one can receive, and I was very happy when it expanded to cover video games in 1998," said Persson.
"When I first heard that I would receive a BAFTA Special Award, I was blown away and deeply humbled. Going to London to accept this award is going to be a very positive and interesting experience that I'm very much looking forward to."
Chair of the BAFTA video games committee Ray Maguire said: "Markus is an inspiration for all games developers and this Award reflects the determination and innovation that he continues to show to both the developer community and to gamers worldwide.
"We are thrilled that he will accept this Award and are excited to see what new developments he will introduce to the industry in years to come."
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First released in early 2009, Minecraft has made over £62 million, allowing Persson to create his own studio Mojang Specifications and secure a partnership with The Lego Group.
Minecraft will release on Xbox Live Arcade this spring, featuring local multiplayer and a tutorial for new players.
It will also be gradually updated to the current PC version but will not launch with Kinect support.
The Video Game BAFTAs will take place on March 16.
View screenshots of the Xbox Live Arcade version of Minecraft below: