David Tennant took over the role of the Doctor in 2005
"This achievement is all thanks to the remarkable production team who first created Doctor Who," said Russell T Davies, who penned the TV revival.
He also thanked the audience "who have kept it alive for all these years".
The series began on 23 November, 1963, and was revived in 2005 after 16 years off the screen.
William Hartnell played the original Doctor Who, with Jon Pertwee, Tom Baker and Peter Davison among those following in his footsteps.
Christopher Eccleston took up the mantle of the ninth Timelord last year - following the show's relaunch. He was replaced after just one series by David Tennant after Eccleston dropped out.
Guinness World Records editor, Craig Glenday, added: "This is a proud day for Doctor fans everywhere."
US series Stargate SG-1, now in its 10th series, holds the world record for "longest-running science fiction show (consecutive)".
It launched in 1997 and has run for 203 episodes without a break. Hit US series The X Files previously held the record, notching up 202 episodes.