Firefighters were called to a three-storey townhouse on Kingston Road, between Galloway Road and Lawrence Avenue East, shortly before 6 a.m. ET.
Two children were initially found without vital signs but were later revived by crews and taken to hospital, according to paramedics.
One of the four children, a 10-year-old boy, later died, police said.
The three other children and their mother are listed to be in critical to life-threatening condition, according to officials.
The fire was knocked down quickly and no other townhouses were affected, according to fire commander Danny MacIsaac.
The fire appeared to have started in the kitchen but the investigation is still ongoing, MacIsaac said, and the fire marshal has been called in.
Peter Rotolo, operations commander with Toronto Parademics Services, said first responders quickly arrived at the scene.
"When you hear something like this, everyone responds appropriately and quickly," Rotolo said.
The incident has also been difficult on first responders because of the involvement of children, both MacIsaac and Rotolo said.