It happened around 3:30 p.m. in the 6900 block of Emlen Street in the West Mount Airy section of Philadelphia.
The 57-year-old male conductor was shot on the platform at the Carpenter Lane Station, police said.
They said there are, however, conflicting reports.
Authorities are working to determine if two teens were refusing to pay the fare or trying to hold up the conductor when an argument occurred.
One witness told police, she heard one of the guys say, "Give me all you got."
And shortly after, that's when one of the teens shot the conductor in the hip.
The conductor was taken to Einstein Medical Center and is listed in stable condition.
Police said the shooter fled the scene.
They are searching for the teens.
Service resumed on SEPTA's Chestnut Hill West Regional Rail Line by Friday evening.