Four people are missing, police said, and they have not been able to confirm the fourth person's whereabouts.
"We're still not totally sure about who is missing and we're working to figure that out. We're working with those who run the home to determine how many were in the house to begin with," Stockholm policewoman Towe Hägg said.
The facility was home to nine people, and eight were taken to the hospital after the fire, the Swedish news agency TT reported.
The fire broke out around midnight and moved quickly, authorities said.
By the time firefighters arrived, there was a hole in the roof and authorities were unable to enter the house.
The home burnt down, and a forensic investigation will begin as soon as the ashes cool, TT reported.
The home was one of 400 of its kind in Sweden that house young people who cannot live with their families.