The boat was located just off of MacMillian Wharf.
Coast Guard crews were on the scene and towed the boat further into the harbor and started extinguishing the flames.
Witnesses say black smoke and flames could be seen coming from the boat.
Cape Cod.com News Reporter Mike DuBour is on-scene and says that so far there have been no injuries reported.
We will have more details when they become available.
A video of the smoke from the boat can be seen below.