The original Naval postgraduate school was established in 1909 for marine engineering, in the time of the Great White Fleet. The original activity was allowed two rooms at Annapolis. In 1912 the program was expanded to include ordnance and gunnery, electrical engineering, radio telegraphy, naval construction, and electrical engineering. Enrollment swelled, to 25. Until 1945, the limited facilities and housing at Annapolis continued.

During World War Two, the Navy concluded that they were overly reliant on civilian institutions, and identified the rapid rate of technical advancement, and Congress backed both a new physical location and full accreditation. A national search followed, narrowing 25 candidate sites to one, a formerly leased hotel complex in Monterey, California. The land was acquired, refurbished, and opened for classes in 1952. 500 students, thousands of pounds of books, many tons of equipment, and faculty travelled cross country in a massive relocation. The new facility solved the school's cramped quarters problem, adding considerable living room, bachelor's quarters, family housing,lab space, lecture space, and the other benefits of adequately sized housing.

Since then, the NPS has added over forty programs in many technical fields, including many highly regarded MS and PhD programs. Particularly notable among these is the Space Systems Academic Group, which has more astronaut graduates than any other program in the world.