The pilot ejected from the plane before the crash and is safe.
The incident happened just after 6:30 pm Wednesday near Dickenson and Cadillac Avenues.
NAS Lemoore says the aircraft was an F-35C fighter jet, which was part of the VFA-125 "Rough Raiders."
Flames were seen coming out of the jet in the middle of a cotton field.
A helicopter arrived at the scene and took the pilot to a nearby hospital for treatment.
Officials say the pilot was an experienced flyer and that the investigation is just getting started.
"This will be a long, drawn out investigation," says Tony Botti with the Fresno County Sheriff's Office.
Fresno County Supervisor Buddy Mendes owns the field where the F-35 went down.
Mendes says he received a call from his son telling him about the crash.
No information has been released on what may have caused the stealth fighter jet to crash.