The fire, located at 7 Sea View Ave. near the intersection with Mission Avenue, was reported around 2:30 a.m., according to San Rafael fire Battalion Chief Jeff Rowan.
When firefighters arrived at the home, they found heavy flames coming from the second floor, Rowan said.
No one was home at the time of the fire and no injuries to firefighters were reported, according to Rowan.
Firefighters were able to bring the blaze under control shortly before 4 a.m., Rowan said.
The cause of the fire remains under investigation.