"Classroom of the Elite" is set in the prestigious Tokyo Metropolitan Advanced Nurturing High School, an institution designed to prepare students for success in society. The school employs a unique class system, dividing students into four classes (A through D) based on their academic and social abilities, with Class A being the highest and Class D the lowest. Students are awarded points equivalent to monetary value, which can be used for various amenities, creating a competitive environment where classes strive to climb the hierarchy.

The narrative centers on Kiyotaka Ayanokōji, a seemingly average and unremarkable student placed in Class D. Despite his reserved demeanor, Ayanokōji possesses exceptional intelligence and strategic thinking, which he conceals to avoid drawing attention. His class, composed of misfits and underachievers, faces constant challenges and discrimination from the higher-ranked classes. Suzune Horikita, a highly capable but aloof student, and Kikyō Kushida, a popular and outwardly friendly girl with a hidden manipulative side, are among the key figures in Class D.

The story unfolds through a series of tests and competitions orchestrated by the school administration, designed to evaluate students' academic, physical, and interpersonal skills. These tests often pit classes against one another, forcing students to navigate complex social dynamics and alliances. Ayanokōji, while maintaining his facade of mediocrity, subtly manipulates events to ensure Class D's survival and success, often outmaneuvering more overtly ambitious students like Class A's leader, Kōhei Katsuragi, and the cunning Class C strategist, Ryūen Kakeru.

As the series progresses, the true nature of the school's system is revealed, exposing its harsh and manipulative methods of molding students into elite members of society. Ayanokōji's mysterious past and the reasons for his enrollment in the school gradually come to light, adding depth to his character and motivations. The interactions between students, their struggles for power, and the moral dilemmas they face form the core of the narrative, highlighting themes of ambition, identity, and the cost of success in a highly competitive environment.