Toronto Police Const. Tony Vella says the teens were shot in the torso early Friday afternoon at a low income housing complex (at 287 Grandravine Drive).
One boy was pronounced dead at the scene early Friday afternoon while police said the second boy died in hospital.
Police have identified the two dead boys as O’She Doyles-Whyte,16, and Kwame Duodu, 15.
Police say witnesses have indicated three males were seen fleeing the scene on bicycles, but there are no details on what prompted the killings.
Toronto Community Housing Board Chair Bud Purves and President and CEO Gene Jones issued a statement saying they are "angered and saddened" by what they call the "tragic loss of young lives to gun violence."
"At the very point in their lives when they should be looking forward to a bright future, too many of our young people are losing their lives to gun violence," said Friday's statement.
The statement says Toronto Community Housing is working closely with police in the investigation.