It was previously reported that the actor had turned down the chance to replace David Tennant.
However, the Sherlock star told The Sunday Times that he had never been in the frame to take over the part.
"I'd turn it down anyway," he insisted. "Jumping onto school stages and saying, 'I am the Doctor', it's not where I want to go."
It was recently confirmed that Sherlock would be returning for a second series.
Meanwhile, Matt Smith will reprise his Time Lord role in the forthcoming Doctor Who Christmas special.