The shots were fired at Lenox Avenue and West 139 Street just before 10 a.m., and police believe the teen was the intended target.
He was grazed in the head as he boarded the M1 bus, ad he was treated at the scene before being rushed to NYC Health + Hospitals/Harlem.
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His injuries were described as minor.
Iesha Sekou, the founder and CEO of Street Corner Resources, a stop the violence non-profit, visited him in the hospital and said he is going to be OK.
"This young man was really blessed, blessed to not have the bullet penetrate his skull," she said. "We weren't surprised there was a shooting. The only surprise was that it was happening so early."
The 39-year-old bus operator was directly behind where the shooting took place, but he was reportedly protected by the shield placed around the driver's seat.
A second round struck the windshield.
"My heart goes out to the bus operator," interim NYC Transit President Craig Cipriano said. "What a traumatic experience this must have been. Out of the grace of God, we know that he did not suffer any physical injuries. My heart goes out to him."
The bus operator was hospitalized for trauma and a minor injury to his left hand.
The suspect fled the scene, and no arrest were immediately made.
The investigation is active and ongoing, and anyone with information is asked to call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782).
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Shootings involving children and teens are up by a lot, as more than 100 non-fatal shootings involving kids under the age of 17 have happened so far this year.
That's more than double the amount from 2019.
"Youth violence is a high priority for the NYPD," Deputy Chief Russell Green said. "As a matter of fact, most of the members of the service behind me, we just returned from a youth violence strategy meeting held this morning at One Police Plaza."
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