The Naval Academy Museum was built in 1939 through the generosity of the Naval Academy Athletic Association and the Naval Institute. These organizations responded to the offer of Colonel Henry Huddleston Rogers to donate his collection of historic ship models to the Naval Academy by funding the construction of the Museum. Very soon, the ship models found other homes, such as in Mahan Hall where they graced the lobby and entry to the former library on the second deck, and in academic buildings throughout the yard. In their place, artifacts and works of art relating to the history of the U.S. Navy and of the Naval Academy have helped to inspire generations of midshipmen and help them relate to the history and heritage of those who have served before them.

Initially the Museum exhibition spaces occupied only the front portion of the main floor of the building; the back gallery room was an addition to the building in the 1960s. The back gallery now houses the exhibition "100 YEARS and forward..." While the Main Hall of the Museum has not significantly changed is appearance in many years, the objects on exhibit are in constant rotation. The Main Hall exhibitions contain some of the most important artifacts in the collection: artifacts from famous ships such as USS Constitution and USS Monitor, and memorabilia of early leaders such as Edward Preble, Isaac Hull, two Perry brothers, John Dahlgren, and William Halsey. The exhibitions continue to inspire midshipmen and visitors with the historic and continuing contributions of the United States Navy and the Naval Academy.