Officially sanctioned by the BBC, the magazine began life as Doctor Who Weekly in 1979, published by the UK arm of Marvel Comics. The first issue's cover date was 17 October, with a cover price of 12p; however, due to the practice of forward dating magazine covers to provide greater longevity on the shelves, its actual release date was 12 October.

The magazine moved from weekly to monthly publication with #44 in September 1980, becoming Doctor Who (the tagline A Marvel Monthly was not part of the name, but simply a description which appeared on many of Marvel UK's monthly titles at that point) and a cover price of 30p. The title changed to Doctor Who Monthly with #61 and Doctor Who Magazine with #85 in February 1984. In 1990 it started appearing once every four weeks (13 times a year). Despite the BBC discontinuing production of Doctor Who in 1989, the magazine continued to be published, providing new adventures in the form of comics. The television programme was revived in 2005, providing a new generation of fans which the magazine is seeking to attract.

DWM features an ongoing comic starring the current incarnation of the Doctor, though for a period between 1989 and 1996, when the series was off the air, it featured previous Doctors. Notable writers and artists who have worked on the comic include John Wagner, Pat Mills, Alan Moore, Dave Gibbons, Mike McMahon, John Ridgway and Ian Edginton. Selected stories from the comic were also reprinted in North America by Marvel Comics. Supporting characters that have crossed over from the comic to other spin-off media include Frobisher, the shape-changing companion of the Sixth and Seventh Doctors; Abslom Daak, the Dalek Killer; the Special Executive who would later appear in Marvel's Captain Britain; and the villainous Beep the Meep.

The magazine has also featured other comics over the years, most notably "Doctor Who?", a humorous look at the series by Tim Quinn and Dicky Howett. This was principally a three-panel comic strip, though occasionally page-long parodies were featured. In the 1990s a secondary serious comic was featured on the inside cover; for many issues this was "The Cybermen", a series of tales set on Mondas prior to the events of The Tenth Planet, explaining the back-history of the Cybermen. The TV21 comic "The Daleks" was also resurrected, continuing the story from where it had left off by showing the Daleks attacking Earth; it was drawn in the same style as the 1960s original.