The actress will succeed Peter Capaldi who is stepping down this Christmas in a special episode which also stars David Bradley as the First Doctor, originally played by William Hartnell between 1963-66.
Bookmakers had previously suggested former Death in Paradise star Kris Marshall and Phoebe Waller-Bridge were the favourites to take over as the show’s lead but in the last 24 hours Whittaker took pole position.
Talk of a gender swap has been a constant since the 1980’s when then producer John Nathan-Turner suggested outgoing Doctor, Tom Baker, could be replaced with a woman.
While fans large largely shrugged off such talk in the past, the decision by show boss Steven Moffat to replace John Simm as the Master with Michelle Gomez has increased the chances of a female Doctor.
Whittaker will be joined at Doctor Who’s Cardiff production base by Chris Chibnall who also wrote and created Broadchurch.
Chibnall takes over from outgoing show runner Steve Moffat who, like Capaldi, steps down at Christmas.
Whittaker said: “I’m beyond excited to begin this epic journey with Chris and with every Whovian on this planet.
“It’s more than an honour to play the Doctor. It means remembering everyone I used to be, while stepping forward to embrace everything the Doctor stands for: hope.
“I can’t wait.”
Chibnall added: “I always knew I wanted the Thirteenth Doctor to be a woman and we’re thrilled to have secured our number one choice.
“Her audition for The Doctor simply blew us all away.
“Jodie is an in-demand, funny, inspiring, super-smart force of nature and will bring loads of wit, strength and warmth to the role.
“The Thirteenth Doctor is on her way.”
Whittaker’s casting, which is likely to be controversial with many longterm male fans, has been welcomed by Colin Baker.
The actor, who played the show’s Sixth Doctor, said: “Well I never the BBC really did do the right thing and let the Doctor be in touch with her feminine side. As a father of daughters – result!”