"Fushigi Mahou Fan Fan Pharmacy" centers on a young girl named Kokoro, who works at a magical pharmacy in a fantastical world. The pharmacy, known as Fan Fan Pharmacy, specializes in creating potions and remedies using magical ingredients. Kokoro, alongside her mentor, the skilled pharmacist Fennel, and a talking cat named Sage, embarks on various adventures to gather rare ingredients and solve the problems of their customers. Each episode typically revolves around a specific ailment or issue faced by a character, which Kokoro and her team address by crafting a unique potion tailored to the situation.

The narrative explores themes of empathy, problem-solving, and the importance of understanding others' needs. Kokoro’s journey is marked by her growth as she learns the intricacies of potion-making and the ethical responsibilities that come with wielding magical knowledge. The series balances episodic storytelling with an overarching progression, as Kokoro gradually uncovers more about the world of magic and her own potential. The characters’ interactions and the challenges they face are designed to highlight the value of teamwork, creativity, and compassion. The setting blends whimsical fantasy elements with a grounded focus on the everyday struggles of the characters, creating a charming and accessible narrative.