Three hundred years ago, in the frigid land of Siberia, Jubei Yagyu engaged in a fierce battle with Kitaretsusai of the Northern Yagyu clan. The duel was costly, as his daughter Freesia was frozen in suspended animation. As a result of global warming in the present day, Freesia breaks free from her icy grave and moves to Japan as a middle school transfer student, where she befriends Jiyuu Nanohana. Little does Jiyuu know that Freesia is targeting her to acquire the coveted Lovely Eye Patch, which Freesia believes is rightfully hers.

The series is set in the distant future in which the Earth is split in two. The southern hemisphere is placed in another dimension while the inhabitants of the northern hemisphere are able to morph into beast-like humanoids. Eventually the humans of the southern hemisphere, led by Uranus, attack the Beasts. The Three Beasts, Wan Derbard (Wan Dabadadatta) of the Tiger Tribe, Bud Mint (Baado Mint) of the Bird Tribe, and Mei Mer (Mei Mah) of the Mermaid Tribe, are taken prisoner along with Mei Mer's companion Tuttle Millen (Mekka Mannen, also of the Mermaid tribe), but manage to escape thanks to a little girl named Yuuni Charm Password. Together they seek Gaia, which they believe to be a fabulous treasure, but they are pursued by Uranus's minions : V-Darn the vicious mage-knight, V-Sion the warrior woman and Akumako, V-Darn's sadistic imp-like partner.

The series focuses on the main heroine Chiari Tsukikage and her friends on managing the Jewelpet Cafe. One day at the magical world of Jewel Land, Lady Jewelina entrusted Ruby the Magical Jewel Box with a mission to make friends and collect Magic Jewels. At the same time she needs to attend the Jewel Academy to do so and open a shop called the Jewelpet Cafe. However with her friends, things didn't go well as planned with several failed mishaps happened to her and the students being scared, in the point of Ruby giving up. But when she met a young girl named Chiari Tsukikage and decides to help, Ruby's life is about to change forever. Now, she and her friends now must work together for the cafe to prosper, stick together through good and bad luck as well as protecting the Jewel Box from being stolen.

Picture drama episodes included on the DVD/Blu-ray Volumes of Seishun Buta Yarou wa Bunny Girl Senpai no Yume wo Minai.