"Koigakubo-kun Stole My First Time" centers on the relationship between two high school students, Koigakubo and the protagonist, whose first romantic and physical experiences become intertwined in unexpected ways. Koigakubo, a seemingly aloof and enigmatic classmate, unexpectedly confesses his feelings to the protagonist, leading to a series of intimate encounters that blur the lines between genuine affection and manipulation. The protagonist, initially hesitant and unsure of Koigakubo's intentions, finds herself drawn into a complex dynamic as their relationship evolves.

The narrative explores themes of vulnerability, trust, and the emotional turbulence of first love. Koigakubo's mysterious demeanor and past experiences add layers of tension, as his actions often leave the protagonist questioning his sincerity. The story delves into their interactions, highlighting moments of tenderness, confusion, and conflict as they navigate their feelings for each other. Secondary characters, including friends and classmates, occasionally influence the trajectory of their relationship, adding depth to the social dynamics within the high school setting.

As the story progresses, the protagonist grapples with her own insecurities and desires, while Koigakubo's true motivations gradually come to light. The manga balances moments of emotional intimacy with the challenges of communication and self-discovery, creating a narrative that captures the complexities of young love and personal growth. The interplay between the characters' internal struggles and external circumstances drives the plot forward, culminating in a resolution that reflects the evolving nature of their bond.