Police were called just before 10am this morning after the grim discovery in the Old Police Box in Walker Street, in the city.
The man is believed to be in his 30s.
Local residents said the building, next to a black of flats, had been sold off some time ago. Forensic officers were seen carrying items from the single-storey brick building in plastic bags.
The police are saying his death is not believed to be suspicious.
A spokesman for Humberside Police said: “Initial enquiries have been carried out and the death is not believed to be suspicious.
“A file will now be prepared for the coroner.”