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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 comic strips. The television programme was revived in 2005, providing a new generation of fans which the magazine is seeking to attract.

Originally geared towards children, DWM has grown into a more mature magazine exploring the behind-the-scenes aspects of the series. Due to its longevity, it is seen as a source of 'official' and exclusive information, sharing a close relationship with the television production team and the BBC. In 2006, however, it lost its exclusivity when BBC Worldwide launched its own comic, Doctor Who Adventures, aimed at a younger audience.

DWM is now published by Panini Comics, which purchased the title along with the rest of the Marvel UK catalogue in 1995. Panini has begun to digitally restore and reprint older DWM comic strips in graphic novel format. Six volumes have been printed so far: two featuring the comic strip adventures of the Fourth Doctor, one with the adventures of the Fifth Doctor, and three (of a planned series of four) focusing on the Eighth Doctor. Panini also published a one-shot magazine-format reprinting of the complete Ninth Doctor strips in 2006.