The shooting happened around 9 a.m. on the 3100 block of Judson Street.
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The male victim was shot once in the chest, police say. He was taken to Temple University Hospital where he was pronounced dead.
His name has not been released.
E.W. Rhodes school at 29th and Clearfield, where the victim attends, was put on lockdown. The school is about one mile from the shooting scene.
Detectives focused their attention on a PT Cruiser with bullet holes in the windshield. Neighbors say the young man was inside the vehicle when he was shot.
"I got up and was having breakfast and I heard six shots," said Jeanie Philips, who lives on the block where the shooting occurred.
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She said shortly after the 13-year-old was taken to the hospital, family members arrived on the scene to try and figure out what happened.
Philips said a woman approached her.
"She said 'that was my nephew.' She said he had just turned 13 yesterday and that he was on his way to Rhodes over here," she said.
Parents describe adults arriving in a frenzy to pick up their children after they received an alert about the lockdown.
"The kids in school not even safe, like, going to school, coming from school. That's why I always take them to school and from school back," said Chanel Simpson who was picking up her nieces. "Anything could happen. I don't let them go to school by themselves."
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Crystal Higgins said the anxiety parents and children are suffering from over the violence is like never before.
"It's through the roof, my grandkids have to walk to school every morning. This is not living. It's not," said a distraught Higgins.
"It's sad out here for these kids. We've got to watch our babies," said Shawntay Broggins, who arrived at the school with her friend to pick up her friend's daughter.
Philadelphia has logged 1,817 shootings this year. Of those 165 shot were children, and 25 children have been killed by gunfire.