The private yacht was tethered to a dock in the 600 block of 14th Avenue South, and the call came in at 12:44 p.m., authorities said.
The vessel was "partially burned" on the port side, and flames scorched the boat's fiberglass exterior from the steps of the rear dive platform up to the cabin area, Naples Fire Chief Pete DiMaria said.
"It's still smoldering a little bit," he said. "But we got it under control for sure."
No one was on board, and there were no injuries, DiMaria said.
Naples police and fire crews and the Collier County Sheriff's Office responded to the blaze.
The cause of the fire remained under investigation Tuesday.