The series was serialized in Kadokawa Shoten's Young Ace magazine from July 2009 to August 2016 and is licensed by Yen Press.

In this world, Yuki Nagato is not a stoic alien but rather a shy and tentative girl who is a member of North High's literature club alongside Ryoko Asakura, her best friend, and Kyon, whom she has a crush on.

[3][4] On December 18, 2013, which refers to a pivotal date depicted in The Disappearance of Haruhi Suzumiya, the official website for the Haruhi Suzumiya series "vanished" and was replaced by a fake error page containing a hidden link revealing that an anime adaptation of The Disappearance of Nagato Yuki-chan was in production.

[8][9] The series has been licensed for streaming in North America by Funimation (now known as Crunchyroll), who simulcasted the subtitled version as it aired.

[10][11][12] The opening theme is "Fure Fure Mirai" (フレ降レミライ, Pouring Future) by Kitakō Bungei-bu Joshikai (Minori Chihara, Natsuko Kuwatani, Yūko Gotō, Yuki Matsuoka, and Aya Hirano), and the ending theme is "Arigatō, Daisuki" (ありがとう、だいすき, Thank You, I Love You) by Chihara.