The incident happened shortly after 7:00 p.m. at the York Dauphin Station located at 2300 North Front Street.
SEPTA officials say two men got into an altercation along the street.
One man pulled a gun and the other ran up the steps and into the station.
After jumping the turnstile that leads to the platform, the man being pursued was shot at, but not hit.
The projectile struck a westbound market Frankford train.
The suspected shooter fled the scene.
SEPTA police responded.and the train was inspected.
No one was injured.
The investigation is continuing.