Doctor Who Magazine's 2009 issues spanned from issue 403 to issue 415 and were published every four weeks by Panini Comics.

As with previous years issue 413 had 4 difference versions of its cover published, this was part of the magazine's "The Mighty 200" poll on the every Doctor Who television story made. The first cover featured Tom Baker proclaiming on the front "You love City of Death", the second cover featured Peter Davison and proclaimed "You love The Caves of Androzani", the third cover featured Christopher Eccleston and proclaimed "You love The Empty Child" and the fourth featured David Tennant and proclaimed "You love Human Nature.

Tom Spilsbury continued as editor of the magazine.

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