"There are so many people wanting to pretend there is a problem. There isn't," he said, according to Vulture's Twitter. "I wish every single journalist who is writing the alternative would shut the hell up."
Regardless, BBC One published a response addressing some sexist complaints over Whittaker's casting.
"Since the first Doctor regenerated back in 1966, the concept of the Doctor as a constantly evolving being has been central to the programme," they said in a statement. "The continual input of fresh ideas and new voices across the cast and the writing and production teams has been key to the longevity of the series. The Doctor is an alien from the planet Gallifrey and it has been established in the show that Time Lords can switch gender."
ET interviewed Doctor Who alum Karen Gillan on Friday during San Diego Comic-Con, where she shut down the haters as well.
"First of all, if you ever watched Star Trek: Voyager, Captain Janeway came in -- the only female captain -- and absolutely nailed it, so we know that that can work," she pointed out. "And second of all, just relax, it's fine!"
Casting controversy aside, the show also debuted two world premiere videos for fans. The first was the trailer for its annual Christmas special, after which Whittaker's Thirteenth Doctor will be introduced.
The special, titled "Twice Upon A Time," sees the Doctor trapped in a time loop and teaming up with the First Doctor, played by David Bradley. It also hints at the return of actress Pearl Mackie's beloved Bill, who was last seen swirling through the cosmos in an ethereal form.
A touching tribute to Peter Capaldi's time as the Twelfth Doctor was also shown, highlighting his good deeds, and bringing a tear to fans' eyes.
"Twice Upon A Time," will air later this year, and Whittaker will take over the role in 2018.
For more from Karen Gillan on the Doctor Who casting, watch below.