"Classroom of the Elite" is set in Koudo Ikusei Senior High School, a prestigious institution renowned for its nearly 100% university placement and employment rates. The school employs a unique hierarchical class system, dividing students into four classes (A to D) based on their academic and social capabilities. Class A enjoys the highest privileges, while Class D, where the protagonist Kiyotaka Ayanokouji is placed, is considered the least capable and is often marginalized.

Kiyotaka Ayanokouji, the central character, initially appears to be an unremarkable and reserved student. However, it becomes evident that he possesses exceptional intelligence, physical prowess, and strategic thinking, which he conceals to avoid drawing attention. His true abilities are gradually revealed as the story progresses, showcasing his ability to manipulate situations and people to achieve his goals.

The narrative revolves around the school's rigorous and often manipulative system, which pits classes against each other in various academic and physical competitions. These competitions determine the allocation of points, which function as currency within the school, allowing students to purchase privileges and resources. Class D, initially at a significant disadvantage, must navigate these challenges while contending with internal conflicts and personal rivalries.

Key characters include Suzune Horikita, a highly intelligent but socially distant student who becomes a focal point of Class D's efforts to rise through the ranks. Kikyou Kushida, another prominent figure, is outwardly friendly and popular but harbors a manipulative and vindictive nature. Other notable characters include Ken Sudou, a hot-headed athlete, and Airi Sakura, a shy and insecure girl who struggles to fit in.

The story delves into themes of social hierarchy, manipulation, and the psychological pressures of competition. It explores the dynamics of power and the lengths to which individuals will go to achieve success or maintain their status. The narrative frequently challenges the characters' moral boundaries, revealing their true natures under pressure.

As the series progresses, Kiyotaka's mysterious past and the school's hidden agendas come to light, adding layers of intrigue and complexity to the plot. The interactions between characters, their personal growth, and the evolving strategies to outmaneuver rival classes drive the story forward, creating a compelling and thought-provoking narrative.