Demonstrators, claimed by organisers to total 65,000, gathered in the prefectural capital Naha, infuriated with the United States after a former Marine employed as a civilian base worker allegedly raped and murdered a young local woman in April.
The case has intensified longstanding opposition to the bases-a key part of the US-Japan security alliance-on the sub-tropical southern outpost, a popular holiday destination for Japanese and increasingly for China and other Asian countries.
The demonstration was held at an athletics park under scorching heat. Police did not have an immediate crowd estimate.
It began with a moment of silence for 20-year-old Rina Shimabukuro, the murder victim, and a message from her father.
"Why my daughter, why was she killed?" said the message, read on his behalf. "My thoughts are the same as those of all the bereaved families that have met with suffering up to now."
One protester carried a banner reading, "Murderer Marines Out of Okinawa".
Chihiro Uchimura, 71, said she was filled with sadness at Shimabukuro's death.
"As long as there are US military bases this kind of incident will continue to happen," she said.
Rally organisers in Okinawa said similar protests were held throughout the country.
In Tokyo some 3,000 people gathered outside parliament for a rally with some signs reading "No base, no rape in Okinawa" and "Marines, go home".
Hatsuko Aoki, one of the demonstrators, shouted through a microphone: "It's not just a problem for Okinawa. It is a problem for all of Japan."
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