The manga started in July 2014. It currently runs in the monthly magazine GFantasy, and is being published by Square Enix.
Yen Press has licensed to digitally release the manga in English, with the official translated title being Toilet-Bound Hanako-kun. Elex Media has licensed the manga for an Indonesian translation, under the title Hanako Si Arwah Penasaran.
As of March 2020, the manga has 12 volumes in print in Japanese, 9 digital volumes in English (with print editions to be released in 2020), and 10 volumes in Indonesian.
A special edition of Volume 11 was also published concurrently with the regular edition, with a different book jacket design and a mini booklet featuring the "Ghost Hotel's Cafe" event, as does a special edition of Volume 12, featuring a different book jacket design and an original playing card set featuring Hanako-kun characters.
A special volume, titled Volume 0, was also released. The volume contains pilot chapters of Jibaku Shounen Hanako-kun before it was officially serialized, and AidaIro's debut oneshot, Dear My Living Dead.
Square Enix has also published a Jibaku Shounen Hanako-kun artbook, featuring clean versions of previously released artwork and various bonus content.
An anime adaptation by studio Lerche was announced in April 2019. It is currently airing in 2020's winter anime season.
"Hanako-san, Hanako-san... are you there?"
At Kamome Academy, rumors abound about the school's Seven Mysteries, one of which is Hanako-san. Said to occupy the third stall of the third-floor girls' bathroom in the old school building, Hanako-san grants any wish when summoned.
Nene Yashiro, an occult-loving high school girl who dreams of romance, ventures into this haunted bathroom... but the Hanako-san she meets there is nothing like she imagined!
Kamome Academy's Hanako-san... is a boy!