Smoke was seen coming out of the boat, named Risk & Reward, at about 1:30 Wednesday.
Firefighters towed the boat away from the dock and quickly extinguished the fire in the engine compartment. They also knocked out windows on the yacht in order to ventilate the cabin.
No one was injured and it's not known if anyone was aboard the boat.
Firefighters from Sarasota Police Department, Longboat Key Fire Department, Sarasota County Fire Department responded to the fire. The Coast Guard also responded to the incident.