Investigators say the gunman approached the victim, a 37-year-old man, at around 3:00 a.m. along the underground concourse at Broad and Chestnut streets.
The suspect - a tall, heavyset man also in his 30s, wearing a wool cap and having facial hair - shot the victim in the neck.
He then ran off and remains on the loose.
Police heard the victim screaming and rushed to help. He was taken to Hahnemann University Hospital where he was last reported in stable condition.
Investigators initially believed robbery may be the motive, but by late Tuesday morning were ruling that out as a possibility.
The actual motive in this case remains under investigation.