No one was aboard the boat, which had run aground on the south side of Harbor Island Drive, not far from the upscale Coasterra Mexican restaurant.
The fire was reported about 6:10 p.m.
The boat was engulfed in flames when Harbor police officers, who are cross trained as marine firefighters, arrived on a vessel equipped with firefighting gear, Sgt. Scott Ferraioli said.
Harbor police crews and San Diego Fire-Rescue firefighters put out the fire in about 15 minutes, Ferraioli said.
The cause of the fire was under investigation.