South Yorkshire Police said the 13-year-old was trapped in his wheelchair under the car for an hour before he was freed by the emergency services.
A spokeswoman said: “Police are appealing for witnesses after a 13-year-old boy was seriously injured this morning in a collision at Meadstead Drive in Royston.
“A silver Vauxhall Astra is believed to have travelled down Manor Grove towards a T-junction with Meadstead Drive around 11.50am today, Saturday 23 July.
“It’s thought the car went across the junction, through fencing and then through a bedroom window of a bungalow.
“A 13-year-old boy was in the bedroom, sitting at a computer. He became trapped underneath the car for at least an hour and had to be freed by firefighters. Police, doctors and paramedics were also at the scene.”
Two of the boy’s brothers, aged eight and five, and a three year-old sister, who were playing in the bedroom, were slightly injured and taken to Barnsley District General Hospital but not detained.
Police said the disabled boy suffered a broken right leg and was airlifted to hospital in Sheffield, where his condition is described as stable.
The driver, an 82-year-old man, and his male passenger were slightly injured and also taken to hospital.
Police are appealing for witnesses to the accident.