The incident occurred at about 6:30 p.m. PDT on Wednesday, Naval Air Station Lemoore said in a statement.
Specifics about the crash were not made public, but the Navy said the F-35C "went down" not far from Naval Air Station Lemoore, located about 38 miles southwest of Fresno.
"We can confirm the pilot successfully ejected and is safe," it said.
The aircraft was attached to the Strike Fighter Squadron VFA-125, known as the Rough Riders.
It is the second crash involving an F-35 fighter jet so far this year in the United States.
In late January, an F-35 Lightning II aircraft crashed at Alaska's Eielson Air Force Base.
The Air Force said the pilot was safe following the incident.
The F-35C is the fifth-generation of a long-rang stealth fighter jet used by the United States Navy, Marine Crops and Air Force. According to the Navy, it is used to perform air-to-air combat, air-to-ground strikes, reconnaissance and electronic warfare.
The Lockheed Martin-manufactured plane costs between $62.2 million and $77.2 million, according to a December Congressional Research Service report.
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