"Gakkō no Yūrei" is a supernatural horror anime that revolves around a group of students who encounter eerie and unexplained phenomena within their school. The narrative centers on a high school plagued by ghostly occurrences, with the main characters drawn into a series of unsettling events tied to the school's dark history. The story begins with the arrival of a new student, who quickly becomes aware of the school's haunted reputation. Strange sightings, mysterious sounds, and inexplicable accidents suggest the presence of restless spirits.

As the students investigate, they uncover a tragic incident from the school's past involving a student who died under mysterious circumstances. This event is linked to the current hauntings, with the ghost seemingly seeking justice or revenge. The main characters, including the new student, a skeptical classmate, and a teacher with knowledge of the school's history, work together to unravel the mystery. Their efforts lead them to confront the ghost, whose presence grows increasingly malevolent as the truth about the past is revealed.

The plot is driven by a series of escalating supernatural encounters, with each episode revealing more about the ghost's motivations and the school's hidden secrets. The characters face moral dilemmas and personal fears as they navigate the dangerous situation, with their relationships and trust in one another tested. The story builds toward a climactic confrontation, where the students must decide whether to appease the ghost or find a way to banish it permanently. The resolution ties together the themes of guilt, redemption, and the lingering impact of unresolved trauma, leaving a lasting impression of the school's haunted legacy.