In the game's instruction manual, there is an encrypted five-character long code (apparently given to Takamaru by a spy) that reveals the weak point of the game's final boss. The cypher is Japanese Morse code using a combination of hiragana and kanji, and can be deciphered by replacing the hiragana with short vowels, and the kanji with long vowels. The correct answer is Spoiler:"くちのなか" ("kuchi no naka"), or "inside the mouth". In the first printing of Japanese publisher Tokuma Shoten's guidebook however, there was a typo in their copy of the code, resulting in this incorrect answer: Spoiler:"くちのやか" ("kuchi no yaka"). Three months after the game's release, Tokuma Shoten issued an apology in their publication "Family Computer Magazine", stating that the error had been corrected in the second printing of the guidebook onwards; they also included an explanation on how to solve it along with a guide to Japanese Morse code.

In the original game, the screen flashes black, red, and white when the thunder strikes the title screen. The Virtual Console release changes this to a single slower pink flash, as part of the Nintendo re-release tradition of lessening the chance of causing epileptic seizures.

In 1986, Nintendo and Fuji Television produced a 70-minute TV special loosely based on The Mysterious Murasame Castle for the weekly one-shot drama series "Getsuyou Drama Land" (Monday Drama Land). The special, like many other episodes in the later years of the series' run, featured members of the popular J-Pop girl group Onyanko Club as cast members, and starred Masaki Kyomoto as the game's protagonist Takamaru. The special aired once on December 8, 1986, almost eight months after the game's release, and never aired again. It was later released on DVD in 2005 as part of the box set "Onyanko Club in Getsuyou Drama Land DVD Box 2".

The special's existence and DVD release flew under the international radar until 2023, when a user named Ruka, after being prompted in a 4chan thread to verify claims that the special was lost media based on an uncited edit on the game's English Wikipedia article, discovered that copies of the box set were actually being auctioned off on Yahoo! Auctions. Ruka then placed a bid and won a copy, and after circulating it, it was uploaded it to YouTube the following week. With its rediscovery, it's thought to be one of the first live-action adaptations of a video game, and is also the earliest known product to come from Nintendo's collaborations with Fuji, which after this special's airing continued with Yume Koujou: Doki-doki Panic.