The F/A-18D Hornet came down near Marine Corps Air Station Miramar at 11:54 PST, the base said in a statement.
"With a heavy heart, our condolences go to the Marine’s family during this time," according to a statement Friday by the 2nd Marine Aircraft Wing.
The crash site is "on government property east of the air station and there are no indications of damage to property on the ground," an earlier base statement said.
The crashed plane was attached to the Marine All-Weather Attack Squadron 224, based in Beaufort, South Carolina, and had been in California for a training mission, officials said.
The pilot was the only person on board and that Marine's name will not be made public until 24 hours after next-of-kin notification, authorities said.
A San Diego Fire-Rescue Department helicopter helped in the search between 3:48 a.m. and 4:21 a.m. and ground crews were on the scene near Interstate 15 until 6 a.m., officials said.
Search and rescue recovered the body of the pilot at the site, the military said.
The base is about 15 miles north of downtown San Diego.