The 61-year-old star will make a special guest appearance in the hit BBC1 show alongside Jodie Whittaker's 13th incarnation of the Time Lord.
The Mirror reported that fans spotted Fry filming alongside Whittaker in Swansea earlier this week, beg February 18. The comedian was reportedly wearing a tweed '40s style suit while filming, with a TARDIS also spotted in Swansea's Guildhall.
A source from the show has since confirmed Fry's involvement with the new series, which will not air on BBC1 until 2020.
Fry is known to be a devout fan of the show, voicing the Minister of Chance in the "Doctor Who" webcast "Death Comes to Time".
The "Blackadder" actor also wrote an episode for the second series of the rebooted sci-fi show, which was ultimately axed as it was believed to be too ambitious.
Speaking of the upcoming series, showrunner Chris Chibnall recently teased fans with talk of more "action-packed adventures."
"We're off again," he said. "Well we never actually stopped."
"As Jodie Whittaker's Doctor and friends have been winning the hearts of families across the nation this autumn, we've been busy with a whole new set of action-packed adventures for the 13th Doctor."
Chibnall added that the series, Whittaker's second in the iconic role, will be packed with "more scares, more monsters and more Bradley Walsh, Mandip Gill and Tosin Cole" - referring to the Doctor's companions, who are all set to return to the show.