Khurram Rahi, 27, of Rosefield Road, Smethwick, was arrested by police investigating the assault of the girl at Witton station. He is due before Birmingham magistrates on Monday.
A second man, aged 34, who was also arrested on Saturday, has been released while police inquiries continue.
The girl told police she was raped a second time when she left the station.
She flagged down a van for help, police said, but was attacked by the driver, in the early hours of Wednesday.
Det Ch Insp Tony Fitzpatrick, from British Transport Police, said: "This case has gained national interest and I am pleased we are now in a position to charge a man.
"However, we still have a suspect outstanding for the offence in the vehicle.
"I would urge anyone who may have any information regarding this attack to get in touch as soon as possible."
He said the second attack happened at about 02:00 BST near Witton station.
The suspect sought over that assault is described as thick-set Asian man, about 5ft 6in tall with large biceps.
A man has been charged with rape after a 14-year-old girl was attacked twice on the same night in Birmingham.