The pilot escaped unharmed.
The crash disrupted flights to and from the island nation off the coast of Saudi Arabia that's home to the US Navy's 5th Fleet.
Images on social media showed the grey fighter jet's nose tipped into the air but largely intact after what the Navy described as an "uncontrollable" landing.
The F-18 took off from the USS Nimitz, an aircraft carrier now in the Persian Gulf, said Cmdr. Bill Urban, a fleet spokesman. While in flight, the plane suffered an engine malfunction, forcing the pilot to divert, Urban said.
"Due to the malfunction, the aircraft could not be stopped on the runway and the pilot ejected from the aircraft as it departed the runway," the commander said in a statement.
Naval officials began an investigation into the crash and were trying to help the airport resume operations, Urban said.
Bahrain's Transportation and Telecommunications Ministry called the crash landing a "minor incident" in a statement and said flights resumed at the airport several hours later.
Bahrain is also home to an under-construction British naval base.
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