U.S. Air Force Staff Sergeant Timothy Woodland, 24, was charged with raping the woman in June in a case which renewed resentment toward U.S. forces in Okinawa, reluctant host to the bulk of the U.S. military presence in Japan.
Woodland told the district court in Naha, Okinawa's capital, that the woman, in her 20s, had consented to having sex.
Woodland faces at least two years in prison if convicted. He was indicted last month.
A series of crimes over the years by U.S. troops stationed on Okinawa have inflamed tensions and prompted calls for the withdrawal of U-S bases.
A U.S. delay in handing over Woodland to Japanese police had added to the ire of local residents.
Okinawa reluctantly hosts some 27,000 U.S. military staff, around half the U.S. military presence in Japan, and calls have mounted for their reduction following a string of crimes in recent years.
But Okinawa, which has long felt like Tokyo's distant and much put-upon country cousin, may have a louder voice in the future after Masahide Ota, a former governor, won a seat in the Upper House of parliament in elections this summer.
Ota, a U.S.-educated historian, campaigned on a platform that centered around urging a reduction in U.S. forces on the island.
"Okinawa's problems are Japan's," he said, following his win. "I am very glad I gained so much support throughout Japan."
The island is important to the U.S.-Japan security alliance because of its strategic location in the Pacific Ocean between Japan and Taiwan.
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