Higson published many novels through the early to mid-1990s which take a slightly dystopian look at everyday life and have a considerably more adult tone than his other work, with characters on the margins of society finding themselves spiraling out of control. This has led Time Out to describe him as "The missing link between Dick Emery and Brett Easton Ellis".
In 2004, it was announced that Higson would pen the Young Bond series of James Bond novels, aimed at younger readers and concentrating on the character's school-days at Eton. Higson was himself educated at Sevenoaks School, where he was a contemporary of Jonathan Evans, former Director General of MI5. The first novel, SilverFin, was released on 3 March 2005 in the UK and on 27 April 2005 in the US. A second novel, Blood Fever, was released on 5 January 2006 in the UK and 1 June in the US. The third novel, Double or Die, was published on 4 January 2007 having had its title announced the day before. The next, Hurricane Gold, came out in hardcover in the UK in September 2007. In this year he also made a debut performance on the panel show QI. His final Young Bond novel, By Royal Command, was released in hardcover in the UK on 4 September 2008.
Higson is currently writing a post-apocalyptic, zombie-horror series of books for young adults, which has been extremely successful. The eponymous first book in the series, titled The Enemy, was released in the UK by Puffin Books in 2009 and in the US by Disney-Hyperion in 2010. Book 2, The Dead, was released in the UK in September 2010. Book 3, The Fear, was published on 15 September 2011. Book 4, The Sacrifice, was released 20 September 2012. Book 5, The Fallen, was released 12 September 2013. At a school event at Abingdon School on 14 September 2011, Charlie told children: "Originally it was going to be three books and then my publisher, Puffin, said make it five, and now we're up to it being seven." At another, in John Lyon's School, he revealed that the last book in his series would be called The End. This book will come out in 2015 following The Hunted, which was released 1 January 2014.
In 2011, Higson appeared with the original cast (with the exception of Mark Williams) in an online-only version of The Fast Show sponsored by Foster's Lager.