Frank Zappa, in the liner notes of the Mothers of Invention album We're Only in It for the Money, recommends reading the short story before listening to the track "The Chrome Plated Megaphone of Destiny."
Ian Curtis of the band Joy Division was inspired by "In the Penal Colony" to write the song "Colony" from the album Closer.
The novel The Shadow of the Torturer, by Gene Wolfe, follows the exploits of a member of a guild of torturers. At one point, when giving a tour of the facilities to a condemned prisoner, the head of the guild describes a device identical to the one presented in the short story.
The episodic video game Resident Evil Revelations 2 contains many references to Kafka. Along with being set within an island colony, the first episode is named "The Penal Colony" after the story, and a file found within the game contains an excerpt from "In the Penal Colony."