It has been half a decade since Utena Tenjou's parents passed away. However, instead of mourning, Utena vividly remembers the mysterious prince who comforted her in her time of need. That day, the prince—whom she nicknames "Peropero-kun" after he licks her tears away—bestowed upon her a ring and promised that as long as she possesses the keepsake, it would lead her back to him one day.

Since then, Peropero-kun sends Utena a letter once a year just as the roses begin to bloom. Believing the letters are written by Utena's aunt rather than an obscure nobleman, Utena's best friend Kaidou decides to search for evidence that supports his suspicions. When he finds six photos that connect like puzzle pieces in the letters, it proves that not only does Peropero-kun exist, but also that he can be found at the prestigious Ohtori Academy.

Wishing to reunite with her long-lost prince, Utena leaves her current life behind to embark on her search for Peropero-kun. After arriving at the academy, she encounters the Ohtori Academy's student council and their strange treatment of fellow student Anthy Himemiya. Utena's investigation into this shady behavior unleashes a plethora of mysteries that may just lead her to the prince she has sought for so long.

Shoujo Kakumei Utena was published in English as Revolutionary Girl Utena by VIZ Media from January 9, 2002, to March 3, 2004. It was also serialized in their Shoujo anthology magazine Animerica Extra. The publisher re-released the series in a deluxe two-volume hardcover box set.

The series was published in French by Pika Édition; in German by Carlsen Comics; in Italian by Edizioni Star Comics; in Polish by Waneko; in Portuguese by JBC; and in Spanish by Norma Editorial.

The manga has been adapted into various musical and stage productions. It was also adapted into a video game; titled Shoujo Kakumei Utena: Itsuka Kakumei Sareru Monogatari, it was developed and published by Sega in 1998 for the Sega Saturn. The series is known to have influenced particular Western works, such as the critically acclaimed animated TV series Steven Universe.