Doctor Who Magazine's 2003 issues spanned from issue 325 to issue 337 and were published every four weeks by Panini Comics.

Clayton Hickman continued to edit the magazine throughout the year.

As with the previous few years a CD was included with the year's magazines. Unlike previous years, two CDs were included throughout the year (on different issues though). With issue 326 the CD produced by Big Finish Productions featured two stories: the first half of Dalek War: Chapter One, which was part of Big Finish Productions' Dalek Empire series and an original story produced for DWM, No Place Like Home, starring Peter Davison as the Fifth Doctor. With issue 337 the CD (again produced by Big Finish Productions) featured a story and a making of feature: the original story Living Legend starring Paul McGann as the Eighth Doctor and The Making of Zagreus, an audio story celebrating Doctor Who's 40th anniversary. The latter included a slew of actors who had acted in Big Finish Productions' before (and had acted originally in Doctor Who).

Throughout the year the magazine remained at the cover price of three pounds 40 pence (£3.40) in the United Kingdom. From issue 326 the placement of the price, issue, date information and Panini Comics logo were moved from within the box containing the barcode to the top right of the magazine's cover. At the top of this information it stated "Thrilling Adventures in Time and Space".