La famille Sanyo reçoit un jour une surprise de la plus haute importance : Hattori, un petit ninja tout droit venu des montagnes et d'un entraînement intensif, va venir habiter dans leur maison et suivre des cours à l'école élémentaire ! Ninja Hattori-kun suit le quotidien amusant de ce combattant de l'ombre, forcé de cacher sa véritable identité lorsqu'il est en public, et parfois menacé par les membres d'un clan rival au sien…

11-year-old Kenichi Mitsuba is an average kid who goes to secondary school and struggles with his studies, he is very stubborn and is very lazy and therefore always ends up frustrating his parents and teacher. He loves to find an easy way of things. He befriends Hattori Kanzo, a ninja from the Iga Clan, and he becomes part of the Mitsuba family along with his brother, Shinzo and his ninja dog, Shishimaru. Hattori helps Kenichi with his problems, and constantly keeps an eye on him, as a good friend. The main antagonist Kemumaki, a Koga ninja and his ninja cat, Kagechiyo always troubles Kenichi, mainly because of their feud over one girl, Yumeko. Kenichi asks Hattori to take revenge as a recurring storyline in many episodes. Although Hattori is a good friend, Kenichi sometimes fights with Hattori due to misunderstandings created by Kemumaki. Sometimes Jippou, Togejirou and Tsubame help him.