Doctor Who Magazine's 2001 issues spanned from issue 299 to issue 311 and were published every four weeks by Panini Comics. Beginning with issue 307 the Panini Comics logo and web address were included within the barcode/issue/price box on the front of the magazine. This followed the removal of the "Marvel Comics" logo from the magazine the previous year.
Alan Barnes continued as editor of the magazine throughout this year.
A free trading card was included on the front of issue 299 and a free CD which had two audio dramas produced by Big Finish Productions: an edited version of Part One of Storm Warning, an audio story featuring Paul McGann as the Eighth Doctor; and a specially recorded story for release with the magazine, Last of the Titans, which featured Sylvester McCoy as the Seventh Doctor.