"Shōgakusei no Himitsu" centers on the life of a young elementary school student named Riku, who harbors a significant secret: he possesses the ability to see and communicate with ghosts. This ability, which he keeps hidden from his peers and family, often leads him into peculiar and sometimes unsettling situations. The narrative explores Riku's dual life, balancing his ordinary school routine with his encounters with supernatural entities.

The story begins with Riku struggling to understand his unique gift. He frequently encounters spirits lingering in the human world, many of whom are tied to unresolved emotions or unfinished business. These spirits often seek Riku's help to find closure, leading him to navigate complex emotional landscapes and moral dilemmas. Despite his initial reluctance, Riku gradually becomes more adept at assisting these spirits, often learning valuable life lessons in the process.

Key characters include Riku's best friend, Yuna, who remains unaware of his ability but provides emotional support and a sense of normalcy in his life. Yuna's presence highlights the contrast between Riku's ordinary and extraordinary experiences. Another significant character is an elderly ghost named Mr. Tanaka, who becomes a mentor figure to Riku, offering guidance on how to handle his interactions with the spirit world.

The plot unfolds through a series of episodic encounters, each focusing on a different spirit and their unique story. These encounters range from heartwarming to tragic, showcasing a variety of human experiences and emotions. As Riku helps these spirits, he also grows personally, gaining a deeper understanding of life, death, and the importance of empathy.

Throughout the series, the narrative maintains a balance between the supernatural elements and the everyday challenges of childhood. Riku's school life, friendships, and family interactions are interwoven with his ghostly encounters, creating a rich, multifaceted story. The manga effectively blends moments of tension and mystery with themes of compassion, growth, and the enduring impact of human connections.