The following text was removed from the Wikipedia article on the Voynich Manuscript in January 2016:
In the game Broken Sword: The Sleeping Dragon, the Voynich Manuscript contains information about geomagnetic energy that had been used by an ancient civilization. The Cult of the Dragon was able to decipher the manuscript and used it to regain access to geomagnetic energy.
In the game Assassin's Creed IV: Black Flag, the player can collect pages of the Voynich Manuscript as they traverse the game's world. In the game it's revealed that the manuscript was written by the Precursor Race, a species of highly advanced humanoids that created the human race before being destroyed by an apocalypse. In its sequel Assassin's Creed: Rogue, it is revealed that the manuscript is the key to activate a powerful artifact known as Precursor Box, which shows a map that details the location of temples made by the Precursor Race.
In the webcomic xkcd, one strip (593: Voynich Manuscript) deals with the mystery of the manuscript and purports that it was written for an ancient role-playing game in the style of Dungeons and Dragons.
There are likely to be other passing mentions in various contexts.
See also Voynich Manuscript in fiction