"Nekopara" is set in a world where humanoid catgirls, known as Nekos, coexist with humans. The story centers around Kashou Minaduki, a young man who moves out of his family's traditional Japanese confectionery shop to open his own patisserie, La Soleil. Unbeknownst to him, two of the family's Nekos, Chocola and Vanilla, stow away in his luggage, determined to stay by his side and assist him in his new venture.

As Kashou settles into his new life, he discovers the presence of Chocola and Vanilla, who quickly integrate themselves into the daily operations of La Soleil. The narrative explores their efforts to help Kashou run the patisserie while navigating the challenges of living together. The dynamic between Kashou and the Nekos is central to the story, with themes of companionship, responsibility, and mutual support.

The series introduces additional Nekos from the Minaduki household, including the energetic and mischievous twins Azuki and Coconut, the mature and composed Maple and Cinnamon, and the youngest, Shigure, who occasionally visits. Each Neko has a distinct personality and contributes to the shop's success in their own way, often leading to humorous and heartwarming situations.

The plot progresses through a series of episodic events, focusing on the daily lives of Kashou and the Nekos as they interact with customers, face challenges in the patisserie, and deepen their bonds. The narrative emphasizes the importance of family, both biological and chosen, and the value of working together to overcome obstacles.

While the series primarily maintains a lighthearted and comedic tone, it occasionally delves into more serious themes, such as the societal treatment of Nekos and the responsibilities of caring for them. These moments provide depth to the story, highlighting the complexities of the human-Neko relationship.

Overall, "Nekopara" presents a blend of slice-of-life storytelling with elements of fantasy, centered around the endearing relationships between Kashou and his Neko companions. The series captures the charm of everyday life in a world where humans and Nekos coexist, offering a mix of humor, warmth, and occasional drama.