According to earlier reports, police said the 13-year-old was struck by a single bullet round at about 2 p.m. ET Sunday afternoon on Driftwood Avenue, near Jane Street and Finch Avenue, and was taken to hospital with a non-life-threatening injury.
He initially told police it was a drive-by shooting.
Police are now alleging that the 17-year-old gave the younger boy a firearm while inside an apartment building on San Romano Way, and that the 13-year-old accidentally shot himself.
The 17-year-old is accused of helping the 13-year-old to the intersection where he was found and advising him to tell police that he was shot at that location.
The older teen, who cannot be named under the Youth Criminal Justice Act, is expected in court on Monday facing several charges, including possession of a restricted weapon, attempt to obstruct justice and public mischief.