Judy Abbott is an orphan who has been given the opportunity to study at the prestigious Lincoln Memorial High School by a mysterious benefactor whom she only knows as "John Smith". She has only seen his shadow once, and because of his long legs, she calls him "Daddy Long Legs". The only payment she is to give her benefactor is that she write him letters every month, with no expectation of them being responded to.

The anime covers three years of Judy's life, starting with her leaving the John Grier Home orphanage, and ending with her finishing high school.