"Classroom of the Elite" is set in Koudo Ikusei Senior High School, a prestigious institution renowned for its nearly 100% college admission 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 abilities. Class A enjoys the highest privileges, while Class D, the lowest-ranked class, is treated as outcasts. The story primarily revolves around Class D and its students, who are perceived as defective or problematic by the school administration.

The protagonist, Kiyotaka Ayanokouji, is an enigmatic and reserved student placed in Class D. Despite his unassuming demeanor, Ayanokouji possesses exceptional intelligence and physical abilities, which he deliberately conceals to avoid drawing attention. His classmate, Suzune Horikita, is a highly capable but aloof individual who initially distances herself from others, believing her peers in Class D are beneath her. Another key character is Kikyou Kushida, a seemingly kind and popular girl who harbors a manipulative and vindictive side, using her charm to control others.

The narrative explores the school's rigorous and often manipulative system, which pits classes against each other in academic and physical competitions. These contests, known as "special exams," determine class rankings and access to resources, creating a cutthroat environment where alliances and betrayals are commonplace. Ayanokouji, while appearing passive, strategically maneuvers behind the scenes to ensure Class D's survival and growth, often outsmarting both his classmates and rivals from higher-ranked classes.

As the story progresses, the true nature of Koudo Ikusei Senior High School is revealed. The institution serves as a microcosm of society, designed to test and refine students' abilities through extreme challenges. Ayanokouji's mysterious past and connection to the school's underlying experiments gradually come to light, adding layers of intrigue to his character. The series delves into themes of social hierarchy, human psychology, and the ethical implications of manipulating individuals for the sake of progress.

The dynamic between the characters evolves as they face increasingly complex exams and personal dilemmas. Horikita begins to acknowledge the value of teamwork, Kushida's dual nature creates tension within the class, and Ayanokouji's calculated actions challenge the status quo. The interplay of strategy, deception, and growth drives the narrative, making "Classroom of the Elite" a compelling exploration of ambition, identity, and the lengths individuals will go to achieve their goals.