The 90ft Vision II trawler had been docked at the harbour when the fire brigade received a report just after 0130 BST of a blaze on board.
The identity of those who died has not been released, but it is understood they are the crew.
At the height of the blaze, more than 40 fire fighters from four stations were at the harbour.
Grampian Fire and Rescue's David Rout said: 'Our crews were confronted by a severe fire on board the fishing vessel.
'They were subject to intense fire and heat and there were conditions on the vessel which hampered the operation.
'Our search and rescue teams located three fatalities on board the vessel.'
Six appliances were at the scene, including two from Fraserburgh, two from Peterhead, one from Macduff and one from Maud.
Grampian Police said the blaze,which was brought under control by about 0330 BST, did not appear to be suspicious.
Firefighters used eight breathing apparatus and two thermal imaging cameras as they tackled the flames.
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