Okinawa prosecutors charged Christopher Browning and Skyler Dozierwalker, both 23, with raping and injuring the woman last month, Jiji Press said.
Browning is also facing charges of robbing her of money, Jiji said.
The two US sailors, who were reportedly visiting the island from their base on the Japanese mainland, have admitted the rape during questioning, the agency said.
Immediate confirmation of the reports was not available.
The two servicemen allegedly approached the woman before dawn on October 16 on the street in central Okinawa and sexually assaulted her, local media reported, adding the woman suffered neck injuries during the incident.
The case prompted an outcry in Okinawa, the reluctant host to more than half of the 47,000 military personnel Washington has in Japan, and left commanders scrambling to contain the fallout.
US top brass imposed a country-wide nighttime curfew on all servicemen in Japan and announced “core value retraining” would take place.
But weeks later, a serviceman allegedly broke into an apartment and hit a schoolboy in the face after drinking in a village pub in Okinawa during curfew hours.
The alleged incidents come amid swelling protests over the deployment on the island of Osprey aircraft, with locals voicing concerns about the plane’s perceived poor safety record.
In September tens of thousands of people rallied against the tilt-rotor Osprey, which can take off and land like a helicopter and fly like a plane.
Both alleged crimes have provoked street protests, with demonstrators calling for US bases to be shut down.
However, Washington sees the island as a vital strategic stronghold in a region that is increasingly wary of the power of China’s rising military.
In 1995, the gang rape of a 12-year-old Okinawan girl by US servicemen sparked mass protests resulting in a US-Japan agreement to reduce the huge US military presence on the Okinawan chain.