Whittaker, the first woman to play the iconic Time Lord, will be seen for the last time in 2022, with showrunner Chris Chibnall also exiting the beloved TV series.
Before she leaves, the actress will star in a new six-part series later this year (21) and three specials next year (22).
Whittaker paid tribute to Chibnall, the "Doctor Who" production team, and the show's fans.
"In 2017 I opened my glorious gift box of size 13 shoes," Whittaker said in a statement obtained by BBC Online. "I could not have guessed the brilliant adventures, worlds and wonders I was to see in them."
She continued, "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."
"And I cannot thank Chris enough for entrusting me with his incredible stories. 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."
It has not yet been announced who will take over from Whittaker in the leading role.
Outgoing showrunner Chibnall, cast the actress to replace the last Doctor, Peter Capaldi, in 2017.
He 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, and 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."
Whittaker's final feature-length special, where the 13th Doctor will regenerate, will be screened in fall 2022.