Japan's Kyodo news agency said he decided to drive the girl home when she started crying, and that the girl had telephoned her friends for help.
Hirokazu Nakaima, the governor of Okinawa, said he felt "great anger" over the alleged assault.
"I can never forgive such a crime, especially when the victim is a junior high school student."
"I can never forgive such a crime"
Hirokazu Nakaima, governor of Okinawa
A similar incident involving the rape of a 12-year-old Japanese schoolgirl by three US servicemen in Okinawa sparked huge protests in 1995.
The three marines convicted of rape were each jailed between six-and-a-half to seven years.
News of the latest alleged rape comes as the Japanese government tries to persuade residents to accept a plan to relocate a US air base from a densely-populated city in central Okinawa to the coastal city of Nago.
The US Marine Corps in Japan, in an e-mailed statement, said it took the allegation "very seriously" and was fully cooperating with the Okinawa police.
Japan is home to some 50,000 US troops, the bulk of them based in Okinawa, under a mutual security pact.
But residents have long resented bearing what they see as an unfair burden for maintaining the US-Japan security alliance and complain about US military bases causing crime, noise and accidents.
In 2006, Japan and the US agreed to realign US troops in the country including relocating air stations and moving some 8,000 marines from Okinawa to the US Pacific territory of Guam.