A reader of TV Century 21 in his youth, Baxter wrote the Shades of Opinion story TV21 — Almost Perfect!, which featured an in-universe version of himself and mentioned Doctor Who, printed in the magazine in 1968. He later wrote the short story Poyekhali 3201, published as part of Decalog 5: Wonders from Virgin Books, but his story had no links to the Doctor Who universe.
In February 2007, Doctor Who Magazine mentioned that Baxter was slated to write the hundredth release in the main line of Big Finish Doctor Who audio stories. Earthstorm was set to feature the Sixth Doctor, but the script was subsequently "canned" by Big Finish and replaced with another release entitled 100 in the wake of the television series' revival. Baxter went on to use the idea in a (non-Who) story called Project Hades in Asimov's SF Magazine.
SFX reported that Baxter was writing a novel for BBC Books starring the Second Doctor, (SFX Collection 47) later confirmed as being The Wheel of Ice, which was released in hardcover on 16 August 2012.
Baxter also wrote an introduction to the 2011 publication of Doctor Who and the Abominable Snowmen novelisation and contributed to the charity reference book Behind the Sofa: Celebrity Memories of Doctor Who.