The show, which was revived in 2005, having originally made it debut in 1964.
Showrunner Stevan Moffat said the episode would bring a “whole new dimension of adventure for the Doctor to explore”.
The birthday edition on November 23rd will fall 50 years to the day since the first episode, An Unearthly Child was transmitted.
It will be screened on the BBC HD Channel – BBC One will carry the regular high definition broadcast – as well as in cinemas.
The BBC has previously experimented in 3D through coverage of Wimbledon Tennis and broadcast elements of the London Olympics in the format.