In a strange magical world of Little Fairilu lives the Fairlu: small magical fairies representing flowers, insects and other entities born from the Fairilu Seed. Each of the Fairilu are born with their own key which only fits to a Fairy Door they need to search. If the certain Fairilu finds the right door, they can finally mature into full fairies, which also links them to the human world. But the Fairilu must study and go to school to learn about the world in which they live while meeting new friends.

The anime series focuses on Lip, a newly born Flower Fairilu and on Nozomi Hanamura, a 12 year old middle school student who loves flowers and once learned about the magical creatures from his grandmother, believing that they existed and researches them. The series follows Lip's overall life in Little Fairilu as told by Nozomi's experience, watching and narrating how did she grow up into a full-pledged fairy while making friends and learning from everything around her.