To address this "big problem," the company, which is owned by Ebay, has enlisted the Space Tourism Society and the SETI Institute to help it launch PayPal Galactic (yes, that's the real name), an initiative to devise solutions.
(Read More: The Next PayPal? Stripe Cashes In on Online Payments )
Space payments are still at least a decade in the future, Marcus said, but some basic questions need to be answered. For example, he said, "If you become a merchant in space, what is the currency ... that you're going to accept? How do you manage dispute? What's an IP address from space look like? How do you do all of theses things, and what government has regulation authority over space?
"Those are big problems that will take years to be solved, and we just want to start the conversation," he added.
PayPal hosted a conference for its new initiative on Thursday at the SETI Institute to discuss why they were venturing into the space business. Speakers from the SETI Institute, the Space Tourism Society and the Silicon Valley Space Center also voiced the necessity of payments in space at the event.
(Read More: PayPal Makes Moves to Woo Back Start-Ups )
But the guest of honor at the conference was astronaut Buzz Aldrin, who shared his excitement about the growing space tourism industry and PayPal's involvement in helping develop a payment infrastructure.
"The future of space is really limitless and the door to the space frontier certainly has been opened, cracked and we're going to widen it," Aldrin said. "Trailblazers in the private sector have inspired us to think of what is bigger than Earth...We are only a generation away from a permanent human residency on Mars."
—By CNBC's Cadie Thompson. Follow her on Twitter