Takakura Kanba and his twin brother Shoma live together with their younger sister Himari. Their parents are missing and Himari is critically ill. Kanba and Shoina will do anything to make her last days memorable. On a visit to the aquarium, they buy her a cute, yet silly penguin hat. The trip abruptly ends when Himari collapses and dies, but the mysterious force that resides in the penguin hat brings her back to life...temporarily, on the condition that they find the "Penguindrum".

To help them on their quest, each sibling is accompanied by a penguin that only they can see. Unfortunately, these cute penguins are anything but helpful, in their quest to find the Penguindrum, and change Himari's fate.