It happened on the platform at 15th and Market streets around 3:50 a.m. Thursday.
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The male victim was struck in the ankle and leg, police say.
He was able to flag down police near the Clothespin sculpture after being shot.
Both SEPTA and Philadelphia police responded to the scene.
Police say the 18-year-old was taken to the hospital in stable condition.
According to authorities, the victim was with a group of people and the shooting may have stemmed from an argument.
No arrests have been made.
SEPTA Safety
This latest shooting comes just as SEPTA announced a new safety plan to deal with crime, cleanliness and drug use in stations.
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SEPTA officials identified areas where customers reported concerns about homelessness.
They found stations along Market Street, especially at 13th and 15th street stations, and Norristown Transportation Center to be a recurring problem.
SEPTA says the number of homeless people using its stations and trains is rising.
SEPTA's SCOPE program is focused on providing social services to the homeless.
Man, 18, injured in shooting at Center City SEPTA station
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SEPTA officials also promise to secure out-of-sight sleeping locations to discourage loitering and illicit behavior.
Through the SCOPE program, SEPTA has increased the number of patrol officers.
But it only has 210, instead of 260 which is what it's budgeted for.
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SEPTA blames the nationwide hiring challenge, but is confident increased patrols will help lower crime rates.
SEPTA also points out that the use of a powerful tranquilizer known as "xylazine" or "Tranq," which Action News has profiled as a major problem on Philadelphia's streets, may increase the risk of people falling on the tracks.
Keeping stations and trains clean is also a priority. Next year, SEPTA plans to triple its custodial budget.
You can also be part of the solution.
SEPTA says the best thing you can do as a rider is to use its Transit Watch App to report crimes and dangerous situations.
ONLINE: Full SEPTA Report