Born in 1627 as the eldest son of the lumber merchant Tsuruya Shichiuemon in Horikawa, Kyoto. His childhood name was Genkichi. He began studying Zhu Xi learning at eleven, but at twenty-eight, an illness led him to turn over the family business to his younger brother and take the path of devotion to scholarship. For over thirty years thereafter he carried on wide-ranging study of Zhu Xi learning, Buddhism, and Daoism from his home as base, and in later years established his own scholarship, 'kogigaku,' the study of ancient meanings. Rejecting the interpretations of Zhu Xi and the Cheng brothers, he argued that the Analects and Mencius must be read according to the meaning of the ancient words themselves. In 1662 he opened the 'Kogido' at his home in Horikawa and, as a private academy, trained more than three thousand disciples. His principal works 'Gomo Jigi' (1683) and 'Doji-mon' (1691) are regarded as the beginning of a distinctively Japanese Confucianism that broke free from Chinese Confucian dogma. His son Ito Togai brought his father's learning to fruition, and the Ito family transmitted the 'Kogido' for generations. He died in Kyoto in 1705 at 79.

A warm-hearted scholar rich in skeptical spirit. He did not simply reject Zhu Xi learning but, through deep reading, became a thinker who concluded that 'it differs from the teaching of Confucius and Mencius.' Prizing everyday life, he held fast to a way of living in which life and learning coincided. Reinterpreting 'jin' (benevolence) as 'love,' he turned Confucianism from an abstract theory of morality into a practical philosophy of human affection. His disciples included Kyoto townsmen, samurai, and physicians — a wide variety of people — and he spread a Confucianism 'of human feeling.'

The Kogigaku school, together with Ogyu Sorai's Kobunjigaku, made up the twin peaks of 'kogaku' (ancient learning) and was the first challenge to the establishment of Zhu Xi as official doctrine. The methodology of 'Gomo Jigi' is appraised as a forerunner of modern philology, reading texts in their historical context. Developed by his son Togai and grandson Rangu, the Kogido at Horikawa continued as a stronghold of Kyoto Confucianism for 240 years until 1904. Today the site of the Kogido in Kamigyo Ward, Kyoto, is preserved as a historic site. Since Meiji it has been reappraised as the starting point of a Japanese rationalism in the modern intellectual history of Japan by such scholars as Tsuda Sokichi and Maruyama Masao.