The long-rumoured project - which has the working title An Adventure in Space and Time - will focus on the creation of the popular sci-fi drama in 1963.
Steven Moffat and Mark Gatiss arriving for the Arqiva British Academy Television Awards 2012 at the Royal Festival Hall, London.
Mark Gatiss will script the 90-minute special, which will be produced by the BBC's drama unit in Wales and air on BBC Two in 2013.
"This is the story of how an unlikely set of brilliant people created a true television original," said Gatiss. "And how an actor - William Hartnell - stereotyped in hard-man roles became a hero to millions of children.
"I've wanted to tell this story for more years than I can remember! To make it happen for Doctor Who's 50th birthday is quite simply a dream come true."
Doctor Who executive producers Steven Moffat and Caroline Skinner will also oversee the project, which has been compared to BBC Four's 2010 biopic The Road to Coronation Street.
Moffat said: "The story of Doctor Who is the story of television, so it's fitting in the anniversary year that we make our most important journey back in time to see how the TARDIS was launched."
The showrunner previously told Digital Spy that plans were already underway for the show's anniversary on November 23 next year.
A production and transmission schedule for An Adventure in Space and Time will be confirmed next year, along with casting.
Doctor Who is expected to return to BBC One for its seventh series later this month.
