The Spanish began building a fort at the base of Point Guijarros, opposite the tip of North Island (Coronado).

Samuel Du Pont, entered the abandoned land where the fort once stood and raised the American flag.

In February 1852 President Millard Fillmore set aside the southern portion of Point Loma of about 1,400 acres (6 km2) for military purposes.

Starting in April 1995, several commands were decommissioned or their homeports were changed to meet the post-Cold War downsizing requirements of the Navy.

Commands throughout San Diego were regionalized to provide equal or better base services while managing a reduced budget.

On March 13, 2023, Naval Base Point Loma was visited by President Joe Biden along with the prime ministers of Australia and the United Kingdom.