The noon rally began with the protest version of a torch lighting in United Nations Plaza. Then the march began to nearby San Francisco City Hall.
"We're not against the Olympics, we're against violations of human rights," said Samten Chinkarlaprang, a Tibetan who owns a Berkeley cafe. She was participating in the protest with five friends from Minneapolis. They held up a sign that read: "Expose China's Brutality in Tibet."
Protesters marched about one mile to the China Consulate on Laguna Street.
During the afternoon, a plane flew over the city pulling a banner that read: Stop Cultural Genocide in Tibet."
Another rally and candlelight vigil are scheduled for this evening for the United Nations Plaza.
More protests are planned for Wednesday, when the torch is scheduled to be run through San Francisco.
The Olympic flame was whisked to a secret location shortly after its pre-dawn arrival Tuesday following widespread and chaotic demonstrations during the torch relay in London and Paris. Activists are protesting China's human rights record, its grip on Tibet and support for Sudan despite years of bloodshed in Darfur.
The flame is scheduled to be paraded through the city Wednesday on a six-mile route that hugs San Francisco Bay.
It began its 85,000-mile journey from Ancient Olympia in Greece to Beijing on March 24, and was the focus of protests from the very start.
The six-mile path currently assigned for the relay is shorter than the courses in Paris and London, making it easier to secure. San Francisco Mayor Gavin Newsom said the amount of time set aside for the relay's opening and closing ceremonies already had been cut, but he would not elaborate.
Newsom said there was a strong likelihood the relay's route would be changed. He said the ultimate decision would be made by Police Chief Heather Fong.
Security was tightened on the Golden Gate Bridge today. On Monday, three protesters scaled the famed span and tied the Tibetan flag and two banners to its cables. Pedestrians and bike riders now must have any large bags checked before they are allowed to cross the bridge.
After San Francisco, the torch is scheduled to travel to Buenos Aires, Argentina, and then to a dozen other countries. The relay also is expected to face demonstrations in New Delhi and possibly elsewhere on its 21-stop, six-continent tour before arriving in mainland China May 4. The Olympics begin on Aug. 8.
The Associated Press contributed to this report. Contact Jessie Mangaliman at firstname.lastname@example.org or (408) 920-5794.