This happened in the area of Trudelle Street and Danforth Road, just north of Eglinton Avenue East, just after 3 p.m.
Police said the motorcyclist turned on a red light and was then hit by a car.
The man, believed to be in his thirties, was taken to a trauma center with fatal injuries.
Police said a gun was originally found at the scene. Later, they determined that it was a BB pistol.
The roads of the region are closed for the reconstruction of the scenes.