Stephenson said that he hoped the sci-fi show's birthday would be a "landmark event" for 2013.
"Last year we have the wonderful Jubilee and wonderful Olympics. This year we have the opportunity to make drama the landmark event for the BBC," he said.
"Everyone has a connection to Doctor Who and we can do something really spectacular with it."
Commenting on the news that Doctor Who will be filmed in 3D for its 50th anniversary, Stephenson described it as "absolutely right" and the perfect example of the "bold innovation" that epitomises the series.
It was announced last night (February 11) that the Who 50th special will be filmed in 3D, with showrunner Steven Moffat promising "a whole new dimension of adventure for the Doctor to explore".
Rumours continue to circulate that the special episode will see former Doctor Who stars return to the series, though Colin Baker - who played the Sixth Doctor between 1984 and 1986 - denied the latest reports last month.
Doctor Who will return to BBC One with new episodes from March 30.