The pilot, identified as Captain Jake Frederick, was located by a Japanese Maritime Self-Defense Force ship, the statement said.
"He is pronounced deceased," it added.
The U.S. military provided few details about the incident, which occurred on Wednesday, other than saying the cause of the crash was under investigation.
The pilot ejected about 120 miles (190 km) southeast of Iwakuni, Japan, the U.S. military said on Wednesday.
The accident occurred on the 75th anniversary of the Japanese attack on Pearl Harbor in Hawaii, which drew the United States into World War Two, Reuters reported.