During the Torchwood Comic-Con panel, he said he would love to appear along-side Matt Smith for the big 50.
"Torchwood and Captain Jack were born from the mother ship, which I always called and referenced as Doctor Who," he said. "I think it would be an interesting thing. I would love to do it.
"If Matt was welcome to it, because he is The Doctor now, I think it would be great. I think it would be a different kind of dynamic there with Jack and The Doctor. So, yes, I'm totally up for it."
John Barrowman has appeared many times in Doctor Who over the years, but he has yet to appear along-side Matt Smith.
"I think it would be disappointing for the 50th anniversary not to have a character like Jack in that show," he said. "Russell thinks it would be a good idea, I've spoken to Steven about it. I love playing Jack, whether with Torchwood or making an appearance on Doctor Who, It's the best coat I could put on every morning.
"It was a dream job for me and [Torchwood co-star] Eve [Myles] and then when they said they wanted to do a spin off show, it was just like being handed our dream job on a platter. We never ever thought we'd be sitting here among people like you. "
Do you want Captain Jack involved in the 2013 anniversary?