The F-35 A Lightning II jet crashed at Hill Air Force Base at 6.15pm local time, the 388th Fighter Wing said in a statement.
The pilot was returning to Hill Air Force Base from a routine training mission when he ejected from the F-35, Col Craig Andrle, commander of the 388th Fighter Wing, said at a news conference.
The pilot was then recovered before being taken to the hospital for observation.
The 388th Fighter Wing said the cause of the crash was under investigation.
The crash sparked a fire that stretched approximately four hectares, Utah Fire Info said. Fire crews were able to contain the blaze, the department said.
The Hill Air Force Base is the Air Force's second-largest by population and geographical size.