It happened around 3:30 Wednesday afternoon in Inyo County east of the Sierra Nevada.
The Air National Guard says the pilot was able to eject safely.
The F-16 Fighting Falcon that went down came from the 144th Fighter Wing in Fresno.
The pilot had 10 years flight experience with the $21 million fighter jet. The California Air National Guard is now looking into the incident.
"When the aircraft malfunctions he tries to save the airplane. When that's not possible then he saves himself. It appears all the systems in the airplane worked correctly because he reached the ground safely," Vice-Wing Commander Col. Clay Garrison said.
The jet crashed in a remote desert area and there are no known injuries on the ground.