Congress established the Bureau in the Department of the Navy by an act of July 5, 1862 (12 Stat. 510), which transferred the hydrographic functions of the Navy's Bureau of Ordnance and Hydrography (1842–1862) to the newly established Bureau of Navigation.
During the early 20th century, BuOrd became involved in the development of aerial weapons. This often led to friction with the Bureau of Aeronautics (BuAer), which had responsibility for the development of Naval aircraft. BuAer's work on "pilotless aircraft," or drones, conflicted with BuOrd's development of guided missiles. After World War II, the Navy examined ways to improve coordination between the two bureaus; ultimately, the decision was made to merge the two organizations into a new bureau, to be known as the Bureau of Naval Weapons (BuWeps).
It was heavily criticized during the Second World War for its failure to quickly remedy the numerous issues with the Mark 14 torpedo which had an over 70% dud rate.
BuOrd was disestablished by Congress by an act of August 18, 1959 (73 Stat. 395), and its functions were transferred to the newly established Bureau of Naval Weapons. BuAir merged with BuOrd to form BuWeps. BuWeps, in turn, was disestablished in 1966 when the Navy overhauled its materiel organization, and was replaced with the Naval Ordnance Systems Command (NAVORD) and the Naval Air Systems Command (NAVAIR). Other systems commands at the time included the Naval Ship Systems Command (NAVSHIPS) and the Naval Electronics Systems Command (NAVELEX). Ship and submarine ordnance functions fell under the new Naval Ordnance Systems Command while air ordnance stayed with the Naval Air Systems Command. In July 1974, the Naval Ordnance Systems Command and Naval Ship Systems Command merged to form the Naval Sea Systems Command (NAVSEA). Traditional Naval Ordnance functions are now conducted at the Naval Surface Warfare Centers which fall under the command of Naval Sea Systems Command.