The woman, a college student visiting her parents in their Spinnaker Point Drive home, awoke to find the intruder in her room at 4 a.m. Sunday, police said.
The woman chased the man downstairs and out of the house, police said. She was unharmed.
Police have not found the intruder, who is described as a Hispanic man in his 20s of average build, standing 5 feet 8 inches tall.
Anyone with information is asked to call San Rafael police at (415) 485-3000.