Police were called to the property at Culduthel Park in the city after a neighbour reported an unpleasant smell.
The flat’s occupant, named locally as 33-year-old Francis Gardiner, had not been seen for around 10 days.
Officers had to force entry to the flat after getting no answer and made the grim discovery.
A Police Scotland spokesman said: “We are conducting enquiries into the death of a 33 year-old man at a flat in Culduthel Park, Inverness, which was reported on Monday.
“The death is being treated as unexplained at this time and a report has been submitted to the Procurator Fiscal.
“Anyone with information regarding this death is asked to contact police on 101.”
He added: “The name of the deceased cannot be released at this stage. Forensic tests are underway to assist in confirming their identity.”