The Broadchurch star succeeds Peter Capaldi, who took over the role in 2013 and leaves in the forthcoming Christmas special.
Whittaker, 35, said it was "overwhelming, as a feminist" to become the next Doctor.
She will make her debut on the sci-fi show when the Doctor regenerates in the Christmas special.
The Huddersfield-born star will find a familiar face for her on set - Doctor Who's new showrunner is Broadchurch creator Chris Chibnall.
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 honor 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."
Dedicated Whovians were quick to react to the news of Jodie Whittaker taking over the Tardis.
On social media, some said it would encourage them to watch the show for the first time - but others said the casting meant they would be switching off, and that the Doctor should be played by a man.
Carla Joanna tweeted to say that she would be tuning in and that the trailer "made me choke up a little". Another tweeter, Ayad, said: "I don't even watch Doctor Who but a woman doctor is so cool."
But Samantha Melton said: "I am a woman and a feminist but I don't want a female Doctor. To me it's trying too hard to tick the boxes."
Doctor Who writer Jenny Colgan, who has written for the series' books and audio dramas, said: "I am of course incredibly excited the new Doctor is a woman; Steven Moffat has been paving the way for this for ages and it is absolutely about time. I can't imagine what it's like for Jodie: she must be so scared and excited all at once, but I couldn't be happier, and 100% can't wait to write for her."
Will Howells, who writes for the Doctor Who magazine and has been a fan for 25 years, said: "In 2017, there shouldn't be anything major about a TV series changing from a male lead to a female one.
"I don't think it's a risky choice at all - but if a show that can go anywhere and do anything can't take risks, what can?"
Actress Olivia Colman, who starred in a Doctor Who episode and was one of the possible candidates for the role, said it was a "classy decision".
"The creatives made the right decision that the part should be a woman and it's about time," she told BBC News. She added that those unhappy about Whittaker being the new Time Lord should "leave her alone and let her do her job brilliantly".
Whittaker starred as Beth Latimer in the three series of the ITV crime drama Broadchurch, as the mother of a murdered boy.
As well as TV work, Whittaker has appeared on the big screen, in One Day, Attack the Block and St Trinian's. She made her film debut in 2006's Venus, opposite Peter O'Toole.
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