He told Anglophenia: "I'd love to see Dame Helen do it - best of luck to whoever gets it, though."
And the BBC has not ruled out casting a woman as the next incarnation of The Doctor once Matt Smith leaves the series.
One bookmaker is offering 25-1 odds on it being the Oscar-winning Queen actress.
However, Mirren has dismissed speculation that she could play the Time Lord. She scoffed at the suggestion, telling AP: "Oh, please - I would put much longer odds on it than that."
But she added that it was time for a woman to play the role.
"I think it's absolutely time for a female Doctor Who. I'm so sick of that man with his girl sidekick. I could name at least 10 wonderful British actresses who would absolutely kill in that role," she said.
Her remarks come after Jenna-Louise Coleman insisted that there's no reason why the new Time Lord in Doctor Who shouldn't be a woman, saying: "I'm not opposed to it. It's about story ideas and what works."
In the interview, The Queen actress Dame Helen also admitted that she "really didn't want to play the role again", and so was "very resistant" about playing the monarch in the play The Audience.
But she added: "It was just an amazing team, and I thought, 'If you walk away from this, you're an idiot'."
Contenders also thought to be in consideration to play the Time Lord include Rory Kinnear, Miranda Hart, Ben Daniels and Samuel West.