Doctor Who Magazine's 2006 issues spanned issue 364 and issue 376 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 produced by Big Finish Productions was included on the cover of issue 367. It was an original story produced for the magazine, The Veiled Leopard, and starred Sophie Aldred as Ace, Philip Olivier as Hex, Nicola Bryant as Peri Brown and Caroline Morris as Erimem.

In a repeat of some previous years' issues, issue 368 was published with two separate covers, as the title noted "His & Hers"; one featured David Tennant and the other Billie Piper on the cover.

With issue 363 the placement of the issue, price and Panini Comics logo returned to within the box with the barcode usually located at the bottom left of the cover.

Throughout the year the cover price remained at three pounds 99 pence (£3.99) in the United Kingdom.

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