- The JSNFRI was established as one of the research institutes of the Fisheries Agency at Nanao, Ishikawa Prefecture, in July 1949.
- Later, the JSNFRI was moved to Bandaijima, Niigata-city, in December 1952.
- The JSNFRI was moved to its present location in April 1965.
- In April 2001 the Fisheries Research Agency (FRA) was established by combining the research institutes of the Fisheries Agency, including JSNFRI, in accordance with the administrative reform policy of the Japanese Government.
- The JSNFRI was reorganized to include the Miyazu, Obama, and Notojima research stations in April 2011.