Princess Tutu is a story within a story. a writer named Drosselmeyer whose stories become reality had his hands cut off and was killed by those fearing his powers. With the story left unfinished, the prince and the raven from one of his stories where trapped in an eternal battle. The raven managed to escape into the outer world and the prince pursued to seal him again. To do so he shattered away his heart. Now the prince was heartless. Drosselmeyer had already written about himself in the story so even after his death he could control the story. So he transforms a duck into a human who saw the heartless prince dancing near the pond. The so called duck's name is Ahiru who could even transfer into Princess Tutu. The whole story is about how the duck tries to join together the shattered hearts and how she is interrupted by her enemies.

During her journey she also meets Fakir who is prince's close friend and Drosselmeyer's descendant. At first even Fakir was against Ahiru but slowly he too becomes an ally and falls for Ahiru.Will Ahiru be able to collect all shattered pieces of heart? What will happen to Ahiru in the end?