There were no injuries in the incident which saw fire service personnel and appliances on site for several hours.
A Scottish Fire and Rescue Service spokesman said: “At 1.33pm on Tuesday, 10 January the Scottish Fire and Rescue Service was called to reports of a fishing vessel on fire at Stornoway Harbour.
“Three appliances were mobilised to the scene.
“Firefighters in breathing apparatus were able to source and contain the blaze with the use of a high pressure water hose.
“We remain at the scene and crews are currently performing cutting away operations to detect any fire spread within the ship.
“There are no injuries.”