The shooting occurred around 9:45 p.m on a northbound Broad Street Line train.
"A male pulled a gun and began shooting," SEPTA Police Chief Tom Nestel. "This is an outrageous event. Somebody pulls out a gun on a subway car with people. A lot of people could have been seriously injured. We are going to make sure that this person is held accountable."
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Police said two teen boys, a 16 and 18-year-old, were both shot.
Police: 2 teens injured after shooting at SEPTA's City Hall station
Both were transported to Hahnemann University Hospital with non-life threatening injuries.
The alleged shooter ran from the scene but authorities blasted out surveillance photos to officers all around the city.
Officials said a 6th District police officer spotted the suspected gunman on the 100 block of North Broad Street and arrested him.
On Thursday, police identifed the suspect as 22-year-old Isaac Orsini.
Orsini is being charged with aggravated assault, simple assault and other related offenses.
It's unclear at this time what sparked the gunfire.
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Anyone with any information is asked to call police at 215-686-TIPS.