Set in the Sengoku Period, Rantarou, Kirimaru, and Shinbei are young students at Ninjutsu Academy, a school dedicated to training aspiring ninjas. Known as "Nintamas" (a blend of ninja and tama, meaning egg), this trio, along with many other students, must master a variety of unique skills to reach their goals. However, things are far from easy, as they frequently struggle with their classes.
With strict instructors like Doi-sensei and Yamada-sensei, playful girls from the Kunoichi class, a crew of pirates, and a host of other colorful characters, the wild world of Nintama is full of surprises.