Police said it is believed the man was inside at the time of the fire in the Dores area near Inverness.
Firefighters were called to the scene at 10.04pm on Monday and extinguished the blaze.
They have not been able to enter the building as it suffered “extensive structural damage”.
A police spokesman said: “The single occupant of the property is currently unaccounted for.
“Inquiries carried out so far indicate the occupant was within at the time of the fire.”
Police and the Scottish Fire and Rescue Service (SFRS) will carry out a joint investigation to establish the circumstances of the blaze.
An SFRS spokesman said: “We were alerted at 10.04pm on Monday May 3 to reports of a house fire in Dores, Inverness.
“Operations control mobilised four fire appliances to the scene to extinguish the fire and assist emergency service partners.”