The anime's concept had been in Jun Maeda's mind long before he was approached in early 2012 by Aniplex's Yōsuke Toba, on behalf of P.A. Works president Kenji Horikawa, to create another anime series after Angel Beats!.

Maeda originally pitched three separate story ideas to Toba; when Toba pointed out one of the other two, Maeda made clear he specifically wanted to make the one that became Charlotte.

The production team deliberately avoided reusing the exact same staff that worked on Angel Beats! in order to bring new variety and prevent the new show from being too influenced by that earlier series.

The title was almost going to be an abbreviation similar to Angel Beats! (which shortens to 'AB'), with a proposed title abbreviating to 'AA', but Maeda rejected it and instead chose 'Charlotte', named after a song by the Japanese band Art-School.

Character designer Kanami Sekiguchi was chosen after producer Kenji Horikawa noticed her work as animation director on episode nine of Angel Beats!.

Director Yoshiyuki Asai was selected partly because of the storyboards he had done for two episodes of Angel Beats!, and the project served as his first opportunity to direct a full series.

The character Jōjirō Takajō was originally designed as an intelligent, bespectacled character, but during development he gradually came to resemble Takamatsu from Angel Beats!.

Voice actress Maaya Uchida was cast as idol character Yusa Nishimori partly because of the positive fan reaction to Angel Beats! voice actors who could sing, and Uchida also performs the in-story band How-Low-Hello's songs.

During recording, Yuu's voice actor Koki Uchiyama was directed to play the character 'more sleazily, in a way viewers would dislike,' while Nao's voice actress Ayane Sakura was told by the sound director to make her performance 'dirty' but not overly violent.

Yuu Otosaka's character design was inspired by Light Yagami from Death Note and Lelouch Lamperouge from Code Geass, aiming for an 'intelligent handsome man' look.

Because the in-universe band Zhiend is meant to be a Western post-rock band, all of their song lyrics are written entirely in English.

Composer Jun Maeda reused some songs he had originally written as a student in the 1990s for the band How-Low-Hello, having conceived them at the time around the concept of 'early B'z'.

Sound director Satoki Iida mixed the show with a more cinematic, movie-like balance than typical anime, pushing the background music more to the forefront.

Character Jōjirō Takajō's superhuman super-speed ability was referenced in a real-world promotional context: it was used at Comic Market 88 to encourage attendees not to run, and he appeared in a collaborative commercial with BS11's mascot character.