The F/A-18 Hornet jet crashed just before midnight local time near Marine Corps Air Station Miramar on Thursday, about 15 miles (24km) from San Diego.
The condition of the pilot was not immediately known. Search and rescue operations are currently underway.
The Marine Corps has launched an investigation into the incident.
In a statement on Friday morning, Marine Corps Air Station (MCAS) Miramar said that the crash site is located on government property just east of the base.
There are no indications of damage to property on the ground, the base's statement added.
Personnel and a helicopter from the San Diego Fire-Rescue Department are assisting in the search, according to NBC News.
"We will provide more information as it becomes available," MCAS Miramar said in the statement.