Frank Zappa, in the liner notes of the Mothers of Invention album We're Only in It for the Money (1968), 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 (1980).
The novel The Shadow of the Torturer (1980) 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 this short story.
Ivan Klíma mentions in his novel Love and Garbage (1986) the first story by Kafka that he had ever read, which was a story of "...a traveler to whom an officer on some island wants to demonstrate, with love and dedication, his own bizarre execution machine."[21] The narrator is very likely referring to "In the Penal Colony".
In Haruki Murakami's novel Kafka on the Shore (2002), the protagonist, a boy who calls himself Kafka, admits that "In the Penal Colony" is his favorite of Franz Kafka's short stories. He imagines Franz Kafka's purely mechanical explanation of the machine as "a substitute for explaining the situation we're in."
The album Public Strain (2010) by Canadian rock band Women features the song "Penal Colony", which references Kafka's story.
The 2015 video game Resident Evil: Revelations 2 contains many references to Kafka's works. Along with being set within an island colony, the first episode is named "The Penal Colony" after the story, a file found within the game contains an excerpt from In the Penal Colony, and one of the locations features a torture device similar to the one described by Kafka.
