Doctor Who Magazine's 2005 issues spanned from issue 351 to issue 363 and were published every four weeks by Panini Comics.

Clayton Hickman continued to edit the magazine throughout the year.

As with previous years a free CD was included on the cover of issue 351 produced by Big Finish Productions it featured two original audio stories The Coup a prequel to UNIT featuring Nicholas Courtney as Alistair Gordon Lethbridge-Stewart and Silver Lining an audio story part of Big Finish Productions' Big Finish Bernice Summerfield series which featured Lisa Bowerman as Bernice Summerfield.

January's issue 351 was the final issue to use the Doctor Who logo associated with the 1996 TV movie and BBC Books' original fiction novel ranges. With issue 352 the magazine moved to a logo that echoed the new series' logo. Along with the new logo the magazine's cover was redesigned with different fonts being used throughout the cover and the change in placement of the issue, price and date information to top left corner. The Panini Comics logo remained on the top right corner of the magazine.

Issue 351 was the only issue with a cover price of £3.40 in the United Kingdom. With the following issue the cover price rose to three pounds 99 pence (£3.99) in the United Kingdom.

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