The actor - who played the eighth Doctor in a 1996 TV movie - told Flicks and the City that, contrary to online rumours, he will not appear in 'The Day of the Doctor'.
"I was a bit dismayed," said McGann. "A bit gutted [not to be asked], but [the older Doctors] are not in it.
"There's all kinds of rumours... doing the rounds. One gets tired of trying to refute things on Twitter and the like, but take it from me - I'm not in it.
"The thing about Doctor Who is... if not now, then maybe some other time. That's the beauty of it - we can always come back."
> Sylvester McCoy on Who 50th: 'Past Doctors haven't heard anything'
McGann also praised the show's new lead Peter Capaldi, who will replace Matt Smith at Christmas, insisting that Doctor Who is "in safe hands".
"Peter Capaldi's going to take over - a proper fan, a brilliant actor [and] a lovely man," he said.
"I think he'll bring the old-fashioned, scary gravitas that my favourite William Hartnell had. He'll bring a fierce intelligence."
Doctor Who's anniversary episode will air on BBC One on Saturday, November 23, and will also be simulcast worldwide and screened in cinemas.
> Paul McGann 'would love Doctor Who return'
Watch a teaser trailer for the Doctor Who 50th anniversary special below: