The boy and his mother, 36, were both hit in the collision, which was reported at about 11:10 a.m. on Saturday.
The child was rushed to Toronto's Hospital for Sick Children and the woman was rushed to Sunnybrook Hospital. She is in life-threatening condition.
Staff Sgt. Brian Bowman said police need to carry out their investigation, but that early indications suggest the collision was a tragic accident.
Police don't believe speed was a factor.
The car ended up straddling the curb in an empty lot near the science centre, which is in the city's northeast near Eglinton Avenue East and Don Mills Road.
Police told CBC News the 39-year-old man is at Sunnybrook Hospital with his wife and is being helped by victim's services.
Police said that language has been a barrier.
Officers with the traffic services unit have taken over the investigation and have video footage of the incident. Witnesses are being asked to contact police.