"Giji Harem" centers on Yuu Nagami, a high school student who, after a traumatic incident in middle school, develops a deep-seated fear of women. This phobia stems from being falsely accused of harassment, which leaves him socially isolated and distrustful of forming relationships with girls. To cope, Yuu creates an imaginary harem in his mind, populated by idealized versions of female classmates and acquaintances. These imagined interactions allow him to navigate his daily life without the anxiety of real-world connections.

The story explores Yuu's internal struggle as he balances his fabricated harem with the complexities of real-life interactions. Key characters include Rin Nanakura, a childhood friend who genuinely cares for Yuu but is unaware of his psychological struggles; Aika Takashiro, a popular and confident classmate who becomes intrigued by Yuu's aloof demeanor; and Saya Mikage, a quiet and observant girl who seems to understand Yuu's inner turmoil better than most. Each character represents a different facet of Yuu's idealized fantasies, yet their real personalities often clash with his projections.

As the narrative progresses, Yuu's imaginary harem begins to blur the lines between fantasy and reality. His interactions with the girls in his life challenge his preconceived notions and force him to confront his fears. The series delves into themes of self-perception, emotional vulnerability, and the impact of past trauma on present relationships. Through its exploration of Yuu's psychological journey, "Giji Harem" examines the complexities of human connection and the ways in which individuals cope with emotional pain. The story maintains a balance between lighthearted moments and deeper introspection, creating a nuanced portrayal of its protagonist's growth.