It happened just before 9 a.m. in the 5200 block of Frankford Avenue.
SEPTA police say they responded to reports of a fight that broke out in the lobby of the transit center.
Officers arrived to find both victims at the scene.
According to SEPTA, one man was shot in the shoulder. The shooter was then shot in the hand by his own gun during a struggle for the weapon.
Both men were taken to the hospital in stable condition. They are also both in police custody.
Anyone with information can call or text Philadelphia police at 215-686-TIPS (8477) or submit an anonymous tip online.