The 44-year-old stated during the Torchwood Comic-Con panel that he would "love" for Captain Jack to celebrate the sci-fi milestone alongside Matt Smith's Time Lord.
"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."
> Read our live blog of the Torchwood panel at Comic-Con 2011 with John Barrowman
Barrowman went on to say that he has already spoken to current Doctor Who showrunner Steven Moffat and former showrunner Russell T Davies about the prospect.
"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."
Barrowman also spoke of his gratitude at being able to continue playing Captain Jack for so long, and identified the time traveller as his "dream" role.
"I love playing Jack, whether with Torchwood or making an appearance on Doctor Who," he added. "It's the best coat I could put on every morning.
"When I was cast as Captain Jack, I thought it would be five episodes of Doctor Who. I thought that was it.
"It was a dream job for me and [Torchwood co-star] Eve [Myles] and then when they said they wanted to do a spinoff 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. "
Barrowman recently claimed that he would enjoy seeing a big-screen adaptation of Torchwood.
More from San Diego Comic-Con 2011:
> Comic-Con 2011: The Walking Dead panel - Live Blog
> Comic-Con 2011: TV Guide Favourites live blog featuring Doctor Who's Matt Smith
> Comic-Con 2011: Dexter panel - Live Blog
> Comic-Con 2011: Shameless panel - Live Blog
Digital Spy is bringing you exclusive videos, pictures and live panel blogs from Comic-Con all weekend - view our full coverage of the event here.
Watch John Barrowman discussing Torchwood: Miracle Day with Digital Spy below: