The actor, who has played the 13th incarnation of The Doctor since 2017, will exit the hit BBC sci-fi series alongside showrunner Chris Chibnall.
Questions about her future with the show began earlier this year, with Jodie now saying in a statement that she had Chris had decided to leave together.
She said: “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. 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.”
Jodie, who made history when she was cast as the first female actor to play The Doctor, added: “I know change can be scary and none of us know what’s out there. That’s why we keep looking. Travel Hopefully. The Universe will surprise you. Constantly.”
Jodie and Chris will leave Doctor Who in what the BBC described as an “epic blockbuster special” to air in autumn 2022, to tie in with the broadcaster’s centenary celebrations.
Chris added: “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. She captured the public imagination and continues to inspire adoration around the world, as well as from everyone on the production. I can’t imagine working with a more inspiring Doctor – so I’m not going to!
Jodie has already filmed the thirteenth series of Doctor Who, consisting of six episodes which will air later this year and also see John Bishop make his debut will as the Doctor’s new companion, Dan Lewis.
The series will then be followed by three specials – the first of which will transmit on New Year’s Day 2022, with another later in spring and the final one will see the Thirteenth Doctor will regenerate in the autumn.
The BBC has said Jodie’s replacement will be announced in due course.