After the unexpected death of her father, 11-year-old Momo Miyaura leaves Tokyo with her mother and moves to an old remote island in Seto Inland Sea. The only memento she has from her father is an unfinished letter with only two words inside: "Dear Momo"—along with her heart's unrest from it.

In the new and unfamiliar small town, Momo reluctantly tries to adjust to the outmoded wooden buildings, silent crop fields, and mysterious isolated shrines. One day, while exploring the attic of her new home, she finds a worn out picture book about youkai. Following this discovery, strange things begin to happen around town, and Momo is greeted by the arrival of three troublesome youkai.

Momo e no Tegami tells the story of a young girl as she struggles to adapt to her bizarre new life and ultimately come to terms with her father's mysterious letter.