Molyneux, who founded development studio Lionhead in 1997, is responsible for games such as Fable, Black And White and Populous, which was developed by his previous studio Bullfrog Productions.
GDC event director Meggan Scavio said: "Peter is a remarkable asset to the games industry, and truly embodies everything that the Lifetime Achievement Award represents.
"We're proud to honour someone who has had such a profound impact on the industry, through his boundless enthusiasm and profound talent in creating games about choice and interactivity that the entire world loves to play."
This year's Game Developers Choice Awards will take place on March 2 and will be hosted by Double Fine's Tim Schafer.
Previous winners of the award include id Software's John Carmack in 2010 and Metal Gear Solid creator Hideo Kojima in 2009.