"Shomin Sample" centers around Kimito Kagurazaka, a young man from a modest background who is kidnapped and taken to Seikain Academy, an elite all-girls school. The academy is dedicated to educating young women from wealthy, sheltered families, preparing them to interact with the outside world. Kimito is chosen as the "commoner sample," a role that requires him to help these sheltered girls understand ordinary life and social norms. To ensure his cooperation, the school fabricates a scenario where Kimito is threatened with castration if he reveals the truth or attempts to escape.

At Seikain Academy, Kimito encounters a group of eccentric and naive students, each representing a different archetype of sheltered nobility. Aika Tenkuubashi, the student council president, is a confident and assertive leader but lacks understanding of basic social interactions. Hakua Shiodome, a shy and reserved girl, struggles with communication and often hides behind her stuffed bear. Reiko Arisugawa, a stoic and disciplined martial artist, is overly serious and unfamiliar with casual relationships. Miyuki Momoki, a cheerful and energetic girl, is overly curious about the outside world but lacks common sense. Karen Jinryou, a self-proclaimed genius inventor, is socially awkward and prone to creating bizarre gadgets.

As Kimito navigates his role, he gradually forms bonds with the girls, helping them overcome their misconceptions and fears about the outside world. Through various comedic and heartfelt situations, the girls begin to develop a better understanding of ordinary life, while Kimito learns to appreciate their unique personalities and perspectives. The series balances humor with moments of genuine character growth, exploring themes of friendship, cultural differences, and the challenges of bridging social divides.

The narrative progresses through episodic adventures, often highlighting the girls' misunderstandings of common societal norms and Kimito's efforts to guide them. Despite the comedic tone, the series occasionally delves into more serious topics, such as the pressures of societal expectations and the importance of empathy. By the end of the series, the characters have grown significantly, with Kimito and the girls forming a close-knit group that transcends their initial differences.