"Gakuen Babysitters" is a heartwarming slice-of-life manga that centers around the lives of Ryuuichi Kashima and his younger brother, Kotarou, following a tragic accident that leaves them orphaned. The brothers are taken in by the chairwoman of Morinomiya Academy, who offers them a place to live on the condition that Ryuuichi helps manage the school's daycare center. The daycare, located on the school grounds, is attended by the young children of the school's faculty and staff, creating a unique dynamic between the high school students and the toddlers.

Ryuuichi, a responsible and nurturing teenager, becomes deeply involved in caring for the children at the daycare, often going above and beyond to ensure their well-being. His younger brother, Kotarou, is a quiet and reserved child who forms close bonds with the other toddlers and gradually opens up emotionally. The story explores their daily lives, focusing on the challenges and joys of childcare, sibling relationships, and the supportive community that forms around the daycare.

The manga introduces a diverse cast of characters, including the other high school students who assist at the daycare, such as Hayato Kamitani, a gruff but kind-hearted boy who becomes Ryuuichi's close friend, and Taka Kamitani, Hayato's younger brother who is one of the daycare children. The toddlers, each with distinct personalities, provide both comedic and touching moments as they navigate their early years under the care of Ryuuichi and his peers.

Themes of family, resilience, and the importance of community are woven throughout the narrative. The story balances lighthearted, humorous moments with poignant reflections on loss and healing, creating a narrative that is both uplifting and emotionally resonant. The interactions between the characters, particularly the bond between Ryuuichi and Kotarou, serve as the emotional core of the series, highlighting the strength of familial love and the impact of kindness in overcoming adversity.