The accident happened at West Broad and Commerce Square Boulevard around 9:00 a.m.
The train was travelling northbound on its way to Trenton.
Police say a woman stepped in front of the train and made no attempt to get out of the way.
The victim was trapped under the train for about 10 minutes before being rescued.
On Friday afternoon, authorities said the woman was in critical but stable condition at the hospital.
Service was delayed for about an hour for the investigation.