The incident occurred around 4:15 p.m. Monday in the tunnel near 22nd and Market streets.
The 54-year-old male victim was taken to Hahnemann University Hospital. His condition has not been released.
According to SEPTA, the employee was working on the trolley tunnel project. The trolley lines run parallel to the Market-Frankford Line in the area.
SEPTA instituted shuttle buses in place of trains on the Market-Frankford Line between 5th and 40th streets shortly after the incident.
The trains returned to normal operation around 5:20 p.m.
LINK: SEPTA.org