The crash took place at 11.54pm local time on Thursday, Marine Corps Air Station Miramar said in a statement. The pilot was the only person aboard.
Search and rescue teams dispatched after the crash discovered the pilot dead at the crash site, according to the the 2nd Marine Aircraft Wing and Marine Corps Air Station Cherry Point in North Carolina.
“With a heavy heart, our condolences go to the Marine’s family during this time,” they said.
The Marines added that the identity of the pilot won’t be revealed “until 24 hours after all next-of-kin notifications have been completed”.
The base said earlier that “the crash site is on government property east of the air station and there are no indications of damage to property on the ground”.
The station said that an investigation has been initiated.
A helicopter from the San Diego Fire-Rescue Department took part in the search efforts from 3.48am until 4.21am and ground crews were present at the scene until 6am, officials said earlier, according to NBC News.
The F/A-18 Hornet is one of the most used aircraft in the Marine Corps. The all-weather fighter and attack plane is known as “the workhorse of Marine Corps tactical aviation,” Naval Air Systems Command stated.
The Miramar base is located 15 miles north of central San Diego.