"Nekopara" is set in a world where humanoid catgirls, known as Nekos, coexist with humans. The story centers around Kashou Minaduki, a young patissier who moves out of his family home to open his own pastry shop, La Soleil. He is accompanied by two Nekos, Chocola and Vanilla, who have been part of his household since childhood. The series explores their daily lives as they navigate the challenges of running the shop while maintaining their unique relationships.

Chocola is energetic, affectionate, and often impulsive, while Vanilla is more reserved, calm, and thoughtful. Their contrasting personalities create a dynamic interplay as they assist Kashou in his culinary endeavors. The narrative delves into the bond between humans and Nekos, highlighting themes of companionship, responsibility, and mutual care. As the story progresses, other Nekos from Kashou's family, including his younger sister Shigure and her Nekos, Azuki and Coconut, become involved, adding layers to the interactions and expanding the cast of characters.

The plot is episodic, focusing on slice-of-life moments and lighthearted situations, often revolving around the preparation of desserts, the operation of the shop, and the Nekos' playful antics. While the series maintains a predominantly cheerful tone, it occasionally touches on deeper themes, such as the societal roles of Nekos and the emotional connections they share with their human counterparts. The narrative avoids heavy drama, instead emphasizing the warmth and humor of the characters' everyday lives. Through its focus on the relationships between Kashou and the Nekos, "Nekopara" presents a heartwarming portrayal of coexistence and the joys of shared experiences.