Doctor Who Magazine's 1999 issues ran from issue 273 to issue 285. They were published every four weeks by Panini Comics, although covers were still branded with the "Marvel Comics" logo. With issue issue 279 the placement of the logo shifted from the top right corner to within price/issue/barcode box (usually located in the bottom-left corner).

Gary Gillatt and Alan Barnes continued as co-editors of the magazine.

For the 20th anniversary of the magazine, issue 283 was released as two separate, magazines each with a different cover. Tom Baker featured on one cover and Paul McGann featured on the other. This was the first time that the magazine had produced two separate covers for the magazine.

Talking 'Bout My Regeneration CD cover

From issue 273 through to issue 278 the magazine used the "diamond" Doctor Who logo. With issue 279 they changed to the logo used in the 1996 television movie starring Paul McGann. This logo was being used by BBC Books for their Eighth Doctor Adventures and Past Doctor Adventures novel ranges and by Big Finish Productions for their Doctor Who audio drama range.

A CD was included with issue 279, attached to the front of the magazine. This was a promotional CD from Big Finish Productions titled "Talking 'Bout My Regeneration". This was the first time since issue 167 that a free audio disc had been included with the magazine (with issue 167 it had been a record-like "FlexiDisc"). It began a trend for Big Finish Productions to give away free CDs featuring original content developed for the magazine and a sampling of their available audio stories.

For all of this year's issues the cover price in the United Kingdom remained at three pounds twenty pence (£3.20). Its page count remained the same, despite December 1998's issue also being £3.20 and having an extra 13 pages for a total of 68 pages (January 1999's issue 272 had 51 pages).