The star – who became the first woman to play the Time Lord when she took over the part in 2017 – will leave the BBC sci-fi show next year.
The announcement comes following speculation about her saying goodbye to the Tardis.
Whittaker said in a statement: "In 2017 I opened my glorious gift box of size 13 shoes. I could not have guessed the brilliant adventures, worlds and wonders I was to see in them."
She went on: "My heart is so full of love for this show, for the team who make it, for the fans who watch it and for what it has brought to my life."
The actor, 39, also praised showrunner Chris Chibnall, who is leaving the programme as well.
"I cannot thank Chris enough for entrusting me with his incredible stories," she said.
"We knew that we wanted to ride this wave side by side, and pass on the baton together. So here we are, weeks away from wrapping on the best job I have ever had.
"I don't think I'll ever be able to express what this role has given me. I will carry the Doctor and the lessons I've learnt forever."
"I know change can be scary and none of us know what's out there," Whittaker added. "That's why we keep looking. Travel Hopefully. The Universe will surprise you. Constantly."
Whittaker will leave the show in autumn 2022, and Chibnall - who cast her in the role - will leave at the same time.
The actor will star in a new series of the programme later this year before leaving in a trio of specials.
The first will air on New Year’s Day 2022, the second will be later in the spring and the third, when the Doctor will regenerate, will air in autumn 2022 and will form part of the BBC’s centenary celebrations.
Chibnall said: “Jodie and I made a ‘three series and out’ pact with each other at the start of this once-in-a-lifetime blast. So now our shift is done, we’re handing back the Tardis keys.
“Jodie’s magnificent, iconic Doctor has exceeded all our high expectations.
“She’s been the gold standard leading actor, shouldering the responsibility of being the first female Doctor with style, strength, warmth, generosity and humour.”
Doctor Who first aired on the BBC in 1963 and always had a male Time Lord at the helm of the Tardis until Whittaker took over four years ago.
Additional reporting by PA.
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