Police were pursuing the car, reportedly stolen from Kam Lake, along the Ingraham Trail when the it veered off the road.
The 12-year-old driver and 10-year-old passenger were hurled from the vehicle.
Sgt. Marion Lamothe, head of the RCMP 'G' Division's major crimes unit in Yellowknife, has been assigned to investigate the incident.
Yellowknife detachment commander Insp. Paul Richards said he will answer questions about the crash when the investigation is complete.
Richard said the youths were released from hospital.
"My understanding is they were fine."