But they say the gunman is still at large.
Investigators say there were a number of students from rival high schools on the train when an argument broke out and shots were fired just before 2:00 p.m. Wednesday.
It happened on SEPTA's busiest line, on a southbound subway train packed with commuters.
"It was just an adrenaline rush for everybody to get out and flee for their safety," said passenger John Solis of Northeast Philadelphia.
Officers arrived at the Susquehanna-Dauphin subway stop on North Broad Street within minutes of the shooting.
They found two boys, ages 17 and 14, injured. Both had been shot while riding on the train. One was hit in the arm, the other in the leg.
"I actually went over to try to help the young males but I was handed back by the police activity, which I understand," Solis told Action News. He said police "were there instantly. I'll vouch for them."
The incident and its aftermath were caught by SEPTA's surveillance system, which police say led them to a man a block away on Carlisle Street.
Action News was there as that man was taken into custody.
Investigators say he's not the gunman, but they believe he was spotted running from the scene.
"It was one of those deals where police were arriving, and people began running, and the police officers chased the people that ran," said SEPTA Transit Police Chief Thomas Nestel. "So we're holding on to those people to see what information they have about the shooting."
Both injured boys were taken to Temple University Hospital. The 14-year-old boy is listed in critical condition. The 17-year-old is listed as stable.
Southbound Broad Street trains were bypassing the Allegheny, North Philadelphia, Susquehanna-Dauphin and Cecil B. Moore stations during the police investigation.
All service had returned to normal by 3:45 p.m.
SEPTA says it works with schools to prevent violence and puts more officers at stops where large numbers of students get on and off.
"We're not going to be at every stop and every train and at some point we have to count on the kids to act accordingly," Nestel said.
The shooting happened an hour before Mayor Michael Nutter's scheduled news conference with US Department of Justice officials on youth violence prevention.
A 16-year-old male was killed in a Tioga Nicetown park last Thursday.
Monday, another young man, also 16, lost his life when he was shot several times in Point Breeze.
Now, Philadelphia will receive two federal grants which will help the city create more programs and come up with strategies to reduce teen violence.
"The strategy will aim to create systemic changes in prevention, intervention and reentry plans," Nutter said.
SEPTA says it does not know which schools today's victims attended or if the shooter was also a high school student.