The fire broke out in the ground-floor flat in Baird Crescent, Leven, at about 11:10.
Police said they were trying to identify the person found in the house.
A spokesman appealed for anyone who was in the area at the time who may have information to contact them.
"Inquires are at an early stage but following a joint assessment of the house by the police and Scottish Fire and Rescue Service, along with an investigation into the circumstances leading up to the fire being discovered, this would appear to be a tragic accident with no suspicious circumstances," the spokesman said.
"We are continuing to make inquiries to identify the person found within the house.
In a separate incident, a man was rescued by firefighters from a bungalow in Sydney Park, Edinburgh, just after 08:30 and taken to Edinburgh Royal Infirmary.
Police have said a fire at a flat in Fife, in which a person died, appears to have been a "tragic accident"