The fire was reported at around 5:30 a.m. on a 30-foot vessel docked near the 2200 block of Shelter Island Drive.
Thirty firefighers with the San Diego Fire-Rescue Department (SDFD) rushed to the scene to find the boat fully engulfed in flames. Smoke was visible from a distance, lingering over the water.
The biggest challenge for crews was gaining quick access to the boat. Officials said they had to lay fire hoses for 700 to 800 feet on the pier leading to the vessel.
Within a half-hour, the boat fire had been knocked down.
SDFD officials said one woman aboard the boat safely escaped the fire, running onto a pier. The woman suffered minor burns but officials said she was treated at the scene and did not want to be taken to the hospital.
Officials believe the fire started in the boat's engine. An investigation will determine more details.
The Harbor Police Department told NBC 7 crews will now work to remove water from the boat so it doesn't sink. The vessel will then be taken to a salvage yard.