1. Msgr. REINERS, Joseph S.V.D. 1912-1926 (Prefect Apostolic)
2. Msgr. CESKA, Anton S.V.D. 1926-1941 (Prefect Apostolic)
3. Msgr. MATSUOKA, Peter Magoshiro 1941-1953
   (1941-1945 Administrator Apostolic)
   (1945-1953 Prefect Apostolic)
4. Msgr. NODA, John Baptist Tokisuke 1953-1961 (Prefect Apostolic)
5. Most Rev. ITO, John Shojiro 1962-1985
6. Most Rev. SATO, Francis Assisi Keiichi O.F.M. 1985-2004

The Prefecture Apostolic of Niigata was established on August 13, 1912 and included the three prefectures of Akita, Yamagata and Niigata that had belonged to the Diocese of Hakodate as well as the three prefectures of Toyama, Ishikawa and Fukui that had belonged to the Archdiocese of Tokyo. It was entrusted to the German Fathers of the Society of the Divine Word.

When the Prefecture Apostolic of Nagoya was established on February 18, 1922, Toyama, Ishikawa and Fukui were incorporated into it.

The first prefect apostolic, Monsignor Joseph Reiners, S.V.D. was succeeded by Monsignor Anton Ceska, S.V.D. in 1926. In 1941 Monsignor Ceska resigned and Monsignor Matsuoka Magoshiro, Prefect Apostolic of Nagoya, became the acting ordinary of the Prefecture Apostolic of Niigata as well. In 1945 he became simultaneously prefect of both apostolic prefectures. In 1953 Father Noda Tokisuke succeeded him as Prefect Apostolic of Niigata. In 1959 Monsignor Noda was nominated first Bishop of Hiroshima, but he excused himself because of illness. He died on October 11, 1961 while still Prefect Apostolic of Niigata. After that, the position of ordinary was vacant, but on April 16, 1962 Niigata was raised to the status of a diocese and in June of the same year Father Ito Shojiro was consecrated bishop and assumed the position of Bishop of Niigata.

Bishop Ito resigned on March 3, 1985, and on June 9 of the same year Father Sato Keiichi, O.F.M. was consecrated bishop .

Bishop Sato resigned and Father Kikuchi Isao was appointed to succeed him on May 14 ,2004.