Born in 1608 as the eldest son of the farmer Nakae Yoshitsugu in Ogawa village, Takashima District, Omi Province (today Takashima, Shiga). At nine he was taken by his grandfather to serve the Kato house in Yonago, and later moved with them to Ozu Domain in Iyo. He studied Zhu Xi learning by himself, and at twenty-seven, resolving to fulfill filial duty to his mother, left his domain without permission, returned home to Omi, and opened a private school. Called the 'Toju Shoin,' the school was open to neighboring farmers and merchants regardless of status, and taught centered on virtues, filial piety, and the Analects. His personality and teaching influenced the villagers, who called him the 'Saint of Omi.' In later years he became absorbed in the Chinese philosopher Wang Yangming's 'Chuanxilu' and became the first major Japanese Yomeigaku scholar. In his principal work 'Okina Mondo' (1640) he criticized the formalism of Confucianism and developed a distinctive philosophy that made 'filial piety' the root of virtue for all. His disciple Kumazawa Banzan led domain reforms in Okayama and demonstrated the practice of Yomeigaku. In 1648 he died of illness at the early age of 40.

Warm, sincere, and humble, he always held 'filial piety' as the first virtue. His plain-spoken lectures were accessible to farmers and townsmen, and he extended his teaching beyond status distinctions. As shown in his resolve to leave his domain for the sake of his mother, he was a practical philosopher whose ideals and actions were one. Though frail in health, his passion for learning and teaching never waned, and his creed was, 'He who would pursue learning must first rectify his own mind.'

As the founder of Japanese Yomeigaku, Toju's thought was transmitted through Kumazawa Banzan into domain reforms at Okayama, and further to the Oshio Heihachiro uprising (1837) and to Saigo Takamori and Yoshida Shoin at the end of the shogunate. After Meiji he influenced Uchimura Kanzo and Mishima Yukio, and his ideas of 'the unity of knowledge and action' and 'attainment of innate knowledge' are being reappraised as an ethical philosophy that still speaks to the present. The site of the Toju Shoin (in Takashima) is preserved as a historic site, and he is still revered locally as the 'Saint of Omi.'