"Boku no Imōto ga Konna ni Eroi Hazuganai" centers around the relationship between two siblings, Kōtarō and his younger sister Yūki. Kōtarō, a high school student, lives a relatively ordinary life until he begins to notice that Yūki, who is in middle school, exhibits behavior that seems unusually flirtatious and provocative toward him. This dynamic creates a series of awkward and comedic situations as Kōtarō struggles to reconcile his role as an older brother with Yūki's increasingly bold and suggestive actions.

The narrative explores the complexities of sibling relationships, particularly the boundaries and misunderstandings that can arise during adolescence. Yūki's behavior often blurs the line between innocent sibling affection and something more ambiguous, leading to moments of tension and humor. Kōtarō, on the other hand, is portrayed as a responsible and protective older brother who is frequently flustered by Yūki's antics but remains committed to maintaining a normal sibling dynamic.

Supporting characters, such as Kōtarō's classmates and Yūki's friends, add depth to the story by providing additional perspectives and interactions. These characters often serve as foils or catalysts for the central sibling relationship, further complicating the situations Kōtarō and Yūki find themselves in. The series balances its comedic elements with moments of introspection, highlighting the challenges of growing up and navigating familial bonds.

The plot progresses through episodic chapters, each focusing on a new scenario or misunderstanding between the siblings. While the tone is predominantly lighthearted, it occasionally touches on more serious themes, such as the pressures of adolescence and the evolving nature of relationships. The manga maintains a focus on character-driven storytelling, with the interactions between Kōtarō and Yūki serving as the primary source of both humor and emotional resonance.