The NRK was founded when Dr. William Danker was officially installed as the first missionary to Japan from the Lutheran Church - Missouri Synod. A special service was held at the Tokyo Chapel Center of the American Army in Kasumigaseki, Tokyo on September 19, 1948.

The Lutheran Hour radio broadcasts, and subsequent correspondence Bible courses, began in 1951. In 1953 the NRK was officially recognized as a religious body in Japan. In 1966 the NRK and Japan Evangelical Lutheran Church (JELC) entered into altar and pulpit fellowship based on their shared faith. Together they have the Japan Lutheran College and the Japan Lutheran Theological Seminary.

In addition to the Japan Lutheran College and the Japan Lutheran Theological Seminary, the NRK also has Urawa Lutheran School (Elementally through High School) in Saitama ad Seibo Gakuen (Junior High / High school) in Hanno, Saitama. A number of congregations continue the tradition of Lutheran education by serving their local communities with preschools and daycares facilities.