The U.S. Naval Undersea Museum was established on July 23, 1979, by the Secretary of the Navy. The following year the Naval Undersea Museum Foundation was formed as a non-profit organization to raise funds to build and outfit a museum facility. Construction of the 68,000 square foot building occurred in stages beginning in 1985 and concluding with completion of the Jack Murdock Auditorium in 1994.

The museum opened as a preview center in 1991 while building construction and exhibit development continued. In 1994, the museum transitioned from a preview center to a fully operational museum.

From its founding in 1979 through 2003, the museum operated as part of the Naval Undersea Warfare Center Division Keyport. Then in 2003, governance of the museum was transferred to Navy Region Northwest as part of a national consolidation of Navy facilities. In 2006, the Navy realigned all of its museums, including NUM, under the authority of the Naval History and Heritage Command (then the Naval Historical Center) in Washington, D.C.

In 2001, the U.S. Naval Undersea Museum achieved accreditation status from the American Alliance of Museums and earned reaccreditation in 2011. With over 39,000 artifacts, the museum is an important repository for information and items related to undersea weapons, submarine technology, diving and salvage artifacts, and undersea vehicle technology. The museum’s 68,000 square foot building contains 18,000 square feet of exhibition space and over 19,000 square feet of collections and archival storage.