Omamori Himari was serialized in Fujimi Shobo's Monthly Dragon Age from June 2006 to September 2013, spanning seventy-five chapters, and was the author Milan Matra's first manga aimed at a general audience.

The chapters were unusually titled using counters for animals ("first one", "second one", etc., using the counter for small animals like cats) instead of the standard "episode 1, episode 2" numbering, even though a new ayakashi didn't appear every chapter.

Several characters, including Kasumori Hisuzu and Kasumori Tobira, originally appeared in the same author's earlier work Higa Toki, serialized in COMIC A-un between 2002 and 2003, while Kuesu Jinguuji first appeared in the author's earlier manga Palladium Garden (2000).

The character Sae Kisaragi was originally planned to secretly be a powerful ayakashi protecting the school and town, who had also erased witnesses' memories of a fight between Himari and Lizlet, but this backstory was scrapped after the author changed the series' direction, something the author later joked about in a bonus chapter.

The homeroom teacher character Yu Shimamura was originally an unnamed background extra in chapter 2, but became a recurring character after the author took a liking to her; her final name was chosen by the author and approved by the voice actress who plays her in the anime, Yui Shimamura, whose own suggestion was to simply remove the character 'nin' from her name.

The recording sessions for the anime overlapped with those of the anime Sora no Otoshimono, since several voice actors (Mina, Iori Nomizu, Asuka Ogame, Tatsuhisa Suzuki, Michiko Neya) worked on both series simultaneously, occasionally causing them to accidentally use character names from the other show during recording.

The anime used the unusual production method of completing the animation footage first and then composing the background music to match it afterward, a technique the official website dubbed the 'Ayakashi Sound System'; this meant the visuals were finished about six months before the show actually aired on TV.

In North America, several volumes of the Omamori Himari manga charted on The New York Times Manga Best Seller List, with Volume 0 reaching as high as No. 4, at one point outperforming a volume of Fairy Tail and a long-charting volume of One Piece in the same week.