Kenichi Shirahama is a good-natured but bullied 15-year-old boy. Tired of being weak, he joins his school's karate club to grow stronger, only to end up as mere target practice for his seniors. However, the beautiful transfer student Miu Fuuriniji changes Kenichi's undesirable fate: she is a first-rate martial artist who introduces him to Ryozanpaku dojo.

There, Kenichi meets the dojo's six eccentric masters, who then decide to take him in as their disciple! Shijou Saikyou no Deshi Kenichi tells the story of history's strongest disciple Kenichi as he trains tirelessly under the world's greatest martial artists—who each specialize in their own martial art—to gain the strength to protect the people and values important to him.