The F-18 crashed while attempting to land on an aircraft carrier in the Celebres Sea, near the Phillipines.
The sole pilot survived by ejecting and landing in the sea, before being rescued by a helicopter crew. He is not seriously injured.
A US military spokesman said: "A pilot safely ejected and was quickly recovered by a helicopter assigned to HSC-4 aboard USS Carl Vinson while conducting routine flight operations during a transit in the Celebes Sea.
A US F/A-18E fighter jet has crashed into the sea
"The incident occurred as the F/A-18E assigned to Carrier Air Wing 2 was on final approach to USS Carl Vinson. The incident is currently under investigation.
"The pilot is being assessed by the medical team on board USS Carl Vinson and there are no apparent injuries at this time."
The jet crashed several thousand miles south of North Korea
Mr Trump announced he had sent an armada to the Sea of Japan, including the downed jet, in a show of force against the hermit state.
He previously refused to rule out attacking the Kim's kingdom, while the bloody despot said he would launch a bloody attack against the US in response.
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Photographer Eric Lafforgue ventured to North Korea six times. Thanks to digital memory cards, he was able to save photos that was forbidden to take inside the segregated state
Eric Lafforgue/Exclusivepix Medi
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Taking pictures in the DMZ is easy, but if you come too close to the soldiers, they stop you
The crash occurred several thousands further south in the Sea of Celebes, near the Phillipines.
Mr Trump had announced the armada was "steaming towards" the Sea of Japan. However, several days after the declaration the group was photographed still thousands of miles away.