The shooting happened around 7:45 p.m. on the 1100 block of Knorr Street.
Philadelphia Police Deputy Commissioner Ben Naish says multiple gunmen came out of an alley on foot and opened fire on the car.
At least nine shots were reported fired into the vehicle, striking the two teens.
The suspects then took off in a getaway vehicle, officials say.
A 14-year-old male was shot multiple times and was transported to Jefferson-Torresdale Hospital in critical condition.
A second teenager, 13, was shot in the arm and taken by private vehicle to Temple University Hospital listed in stable condition.
"It's hard to imagine what could spur somebody else to be coming up and targeting these young people," said Naish. "It's extremely frustrating and concerning for the whole community."
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This shooting comes as gun violence surges in the city, with more than 1,200 shootings in 2021 so far.
It is unknown at this time what led to the incident.
Anyone with any information is asked to call police at 215-686-TIPS.