The pilot was conscious and didn't appear to suffer major injuries, said Maurice Luque, a spokesman for the San Diego Fire-Rescue Department. He was found near the jet, which crashed around noon in an unpopulated, hilly area of the base and triggered a brush fire that burned about 5 acres.
The crash took place just east of MCAS Miramar, officials said, according to CBS News San Diego affiliate KFMB. Miramar is a large station in the northern suburbs of San Diego.
An eyewitness told KUSI-TV the pilot ejected after the nose of the aircraft pitched down, and that the jet plummeted straight down into the ground.
The pilot was apparently the only person aboard, Luque said.
The Marines said the plane crashed about three miles east of the airfield. A spokeswoman, Lt. Katheryn Putnam, did not know if the plane was taking off or landing.
The F-18 is a supersonic jet used widely in the Marine Corps and Navy. The Marines said the cause of the crash was being investigated.