Quadir Jones, 23, is charged with Rape, Involuntary Deviate Sexual Intercourse, Robbery, Aggravated Assault, Kidnapping, and other offenses.
It's not yet known if Jones is responsible for the Thursday morning sexual assault of a 15-year-old girl who was also on her way to school.
The District Attorney's office says they will continue to work with Philadelphia Police on both cases.
The Friday attack happened around 7:45 a.m.
According to police, a 13-year-old girl exited the subway at Broad and Race streets and was approached by Jones who indicated he had a gun.
Police say Jones forced the girl into a parking garage stairway in the 1800 block of Cherry Street where he allegedly raped her.
The D.A.'s office said Jones took the girl's phone and eventually gave it back to her - but only after ordering the victim to give him her number.
The victim was able to get to school and report the rape, the D.A'.s office said.
Jones called and texted the victim, the D.A.'s office said, and Philadelphia Police detectives used location tracking access for the victim's phone number to find Jones and take him into custody later in the day.
Meanwhile, a 15-year-old girl was sexually assaulted around 8 a.m. Thursday.
According to police, the suspect in this case approached the girl while on the Broad Street subway and tried to strike up a conversation.
Police news conference on sex assault of teen girls in Philadelphia
She got off at the Ridge Spur at Broad and Ridge, and the suspect followed the girl while still trying to talk to her.
That's when, police say, the suspect took the girl to an area below a staircase and attempted to sexually assault her.
Police say that attack was thwarted but did not release any further details about how it was stopped.
However, even after the attack was stopped, police say the suspect continued following the girl out onto the street.
Then, police say, the man forced the girl into an apartment where he sexually assaulted her.
The girl notified the school about the attack.
The teen victims do not go to the same school, police said.
Anyone with information is asked to contact Philadelphia police at 215-686-TIPS (8477).