16-year-old high-school gymnast Maron Kusakabe is visited by the angel Finn Fish, who gives her a task. God's power is scattered across the Earth, and if He does not gather enough by the turn of the millennium, He will die. To block Him, The Devil had sent out agents to gather His power, which is the beauty in human hearts, in the form of chess pieces. With Fin's assistance, Maron transforms into the reincarnation of Jeanne D'Arc in order to hunt Demons hidden within works of art. When Maron defeats a Demon, the artwork disappears, and to the outside world it is as if she has stolen it, and she becomes known as a kaitō ("phantom thief"). Maron's best friend is Miyako, the daughter of a police detective in charge of Jeanne's case.

As the series progresses, Maron and Miyako fall in love with new classmate Chiaki, who wants to stop Maron collecting the chess pieces, for he knew that Fin Fish is the Da-Tenshi (Fallen Angel), but apparently in the form of normal angel. Chiaki at first "fakes" falling in love to get closer to Maron, knowing Maron is Jeanne. Later he falls in love truthfully after realising that Maron is worth the effort, even if she does "hate" him. Maron, on the other hand, is confused and does not know what "love" means because her parents abandoned her when she was around ten years old when they were having problems getting along, so no one taught her. As a result, she does not know how to respond to Chiaki's advances.

The manga relates in detail Finn Fish's background, expounding on Fin's relationships with other angels and the events that led to her becoming Maron's partner. This backstory of the angels is not shown in the anime. Kamikaze Kaitou Jeanne has often drawn comparisons to Sailor Moon for the magical girl theme and similarity in appearance between Kaitou Jeanne and Sailor Moon.