The teenager was in a red Vauxhall Corsa which was involved in a collision on the A9 at the junction of the B9161 to Munlochy.
The crash, which took place just before 7pm on Friday evening, also involved a white Nissan Juke and a blue Volkswagen Polo.
The driver of the Polo and the teenager, who was a passenger in the Corsa, were taken to Raigmore Hospital in Invervness.
Police Scotland confirmed the 16-year-old had died as a result of his injuries.
Sergeant Angus Murray, of the Dingwall Road Policing Unit, said: "We are supporting the young man's family at this time and inquiries are ongoing to establish the full circumstances of the crash.
"I would encourage anyone who may have seen what happened to contact us. I would also ask if there are drivers with dash-cam footage which might help with our investigation to call us."