The F 15 Eagle aircraft crashed at around 6.40am on Monday local time, around 80km south of Naha city in the island's south.
The plane was from the US Air Force's Kadena Base, which said on Twitter that its pilot successfully ejected from the plane and was safely recovered by search and rescue teams.
Reports say the pilot suffered a broken leg and was taken by helicopter to a nearby US naval hospital.
There was nobody else in the plane.
Nearly 18,000 Americans and more than 4,000 work on Kadena Air Base, which is home to the 18th Wing and associated US Air Force units, according to its website.
Kadena is the largest US military base in Japan, a country which hosts around 47,000 US troops under a decades-long security pact.
Monday's crash is the latest in a series of incidents involving US military aircraft in Japan, including emergency landings by helicopters, part of a helicopter falling on a school and a fatal crash of an Osprey last year.
