"My Girlfriend's a Geek" centers on the relationship between Taiga Mutou, a straightforward and somewhat reserved office worker, and Yuiko Amamiya, his cheerful and eccentric girlfriend. Yuiko is an avid fujoshi, a term used to describe women who are passionate about boys' love (BL) media, particularly manga and anime. Her obsession with BL becomes a central theme as it frequently influences her behavior and interactions with Taiga, often leading to humorous and awkward situations.

The narrative explores the dynamics of their relationship as Taiga struggles to understand Yuiko's fujoshi tendencies, which include her tendency to imagine romantic scenarios between him and his male coworkers. Despite his initial confusion and occasional discomfort, Taiga gradually becomes more accepting of Yuiko's interests, showcasing his growing affection and patience. Yuiko, in turn, remains deeply devoted to Taiga, though her enthusiasm for BL often overshadows her awareness of his feelings.

The series delves into various comedic scenarios arising from Yuiko's fujoshi lifestyle, such as her attempts to involve Taiga in cosplay, her elaborate fantasies about BL pairings, and her interactions with other fujoshi friends. These moments highlight the cultural aspects of fujoshi subculture while emphasizing the couple's efforts to navigate their differences. Supporting characters, including Taiga's coworkers and Yuiko's friends, add depth to the story by providing additional perspectives on relationships and fandom.

Throughout the series, the relationship between Taiga and Yuiko evolves as they learn to balance their individual interests with their commitment to each other. The story maintains a lighthearted tone, using humor to address the challenges and misunderstandings that arise from their contrasting personalities. By focusing on the interplay between Taiga's grounded nature and Yuiko's vibrant imagination, "My Girlfriend's a Geek" offers an engaging exploration of love, acceptance, and the quirks of fandom culture.