The BBC One sci-fi series will hit the landmark in November 2013, and Barrowman is hoping to reprise his character of Captain Jack Harkness, which he also currently plays in Who spinoff Torchwood: Miracle Day.
"It's the 50th anniversary coming up of Doctor Who and Jack is an integral part to this story and, if I'm going to be a little self-absorbed, I would hope he would be involved, it would be a shame if he wasn't," he told BANG Showbiz.
Barrowman explained that he would be happy to return as Harkness in the original series if the chance arises, but that the final decision will always lie with the BBC and Who's writers.
"I don't think it's a question of whether I would like to come back as Captain Jack, I'd be very happy to do that any time. I know the fans would really like that. But it's a decision left up to the BBC and the drama department.
"So like I've said to all the fans, you need to write to them if you want it to happen because I've never been asked. I know Russell [T Davies] thinks it might be a nice idea as did [executive producer] Steven Moffat but who knows?"
The actor recently announced plans to release a greatest hits compilation titled Tonight's the Night: The Very Best of John Barrowman.
Speaking about the album's tracklisting, he said: "I chose all the tracks because I wanted them to have a personal connection to me. I say in the sleeve each of the songs carry a little piece of my heart with them.
"What I mean by that is the fact that each one has an emotional connection relating to something that happened in my life from my career or to someone who is a family member or the song was introduced to me by a family member. It's a very personal album."
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Take a look at some images from the final episode of Torchwood: Miracle Day below: