Natsume's Book of Friends centers on Takashi Natsume, a teenage boy who has inherited the ability to see yokai, supernatural beings invisible to most humans. This ability, passed down from his grandmother Reiko, has isolated him throughout his life, as others perceive his interactions with yokai as strange or unsettling. After moving to the countryside to live with distant relatives, Natsume discovers a mysterious book called the "Book of Friends," which contains the names of yokai that Reiko had defeated and bound to her will. These yokai are now compelled to serve whoever possesses the book.

Natsume decides to return the names to the yokai, freeing them from their contracts. Accompanied by Madara, a powerful yokai who takes the form of a lucky cat and often goes by the name Nyanko-sensei, Natsume embarks on a journey to locate the yokai whose names are written in the book. Nyanko-sensei initially agrees to help Natsume in exchange for inheriting the Book of Friends upon Natsume's death, but their relationship evolves into a genuine, if often bickering, friendship.

The series is episodic, with each episode or arc focusing on Natsume encountering different yokai and learning their stories. These encounters often reveal the complexities of yokai society and their interactions with humans, as well as the emotional struggles Natsume faces due to his unique ability. While some yokai are malevolent, many are misunderstood or simply seeking closure, and Natsume's compassion often leads him to help them, even at personal risk.

Throughout the series, Natsume's relationships with both yokai and humans deepen. He forms bonds with classmates like Shigeru and Touko Fujiwara, his kind and supportive foster parents, and friends such as Tanuma, who can faintly sense yokai, and Taki, who uses rituals to interact with them. These connections help Natsume gradually overcome his loneliness and mistrust of others, as he learns to rely on and confide in those around him.

The narrative balances moments of melancholy and introspection with warmth and humor, often through Nyanko-sensei's antics or the lighthearted interactions between Natsume and his human friends. Themes of belonging, identity, and the coexistence of humans and yokai are explored as Natsume navigates his dual existence between the human and supernatural worlds. The series maintains a consistent tone of quiet reflection, emphasizing the importance of empathy and understanding in bridging the gap between different worlds.