The era is the Warring States period. Born into a family of low-ranking ninjas for generations, Rantaro enters the Ninjutsu Academy, carrying his parents' expectations for him to become a top-class ninja. There, he meets Shinbei, the son of a wealthy merchant from Sakai, and Kirimaru, who lost his parents in war but lives resiliently. The students of the Ninjutsu Academy are called "Nintama"—ninja eggs. The Ninjutsu Academy is bustling with unique teachers and senior students, including the mysterious genius ninja who is the academy head, the slightly formidable girls of the "Kunoichi Class," and the ninja dog Hemhem! The trio of Rantaro and his friends constantly fail in both classes and exams, and somehow always end up in ridiculous situations. Though the path to becoming splendid ninjas is still long, the Nintama's days are bright, fun, and full of joy!