"Maruhi Megane Danshi Club" centers around a high school club dedicated to the appreciation of boys who wear glasses. The narrative unfolds at Shirogane High School, where the protagonist, Rika, stumbles upon the existence of the Megane Danshi Club. This secretive group, led by the charismatic and bespectacled president, Shintaro, is composed of male students who share a passion for glasses and their aesthetic appeal. The club operates in secrecy, as its members believe their interests are misunderstood by the general student body.

Rika, initially unaware of the club's existence, becomes entangled with its members after accidentally discovering their activities. Intrigued by their unique perspective and the camaraderie among the members, she gradually becomes involved in their world. The story explores the dynamics within the club, highlighting the personalities and quirks of its members, each of whom has a distinct relationship with their glasses. Shintaro, the president, is portrayed as a confident and passionate leader, while other members, such as the shy and reserved Akira and the playful and mischievous Haruto, add depth to the group's interactions.

The plot progresses through a series of episodic encounters and club activities, ranging from discussions about the history and design of glasses to lighthearted competitions and challenges. These events serve to deepen Rika's understanding of the club's ethos and the individual motivations of its members. The narrative also touches on themes of self-expression, acceptance, and the importance of finding like-minded individuals who share one's passions.

As Rika becomes more integrated into the club, she begins to appreciate the unique bond that the members share, despite the occasional misunderstandings and conflicts that arise. The story maintains a balance between humor and heartfelt moments, capturing the everyday lives of the characters as they navigate the challenges of high school while pursuing their shared interest in glasses. Through its exploration of the Megane Danshi Club, the series offers a glimpse into a niche subculture within the school, emphasizing the value of individuality and the joy of connecting with others over shared interests.