Brandon Bostian, 34, was charged with causing a catastrophe and involuntary manslaughter.
He posted $81,000 bail with the promise he will appear in court next month.
Earlier, he was put in handcuffs as he arrived at the 9th district police station with his attorney.
RAW VIDEO: Amtrak 188 engineer Brandon Bostian surrenders
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Just minutes after leaving Philadelphia on May 12, 2015, on a Washington-to-New York run, the train accelerated to 106 mph on a 50 mph curve, derailing in a crash that killed eight people and injured about 200.
The National Transportation Safety Board found that Bostian essentially forgot where he was when he sped up.
Bostian, who has been on unpaid administrative leave from Amtrak, did not respond to reporters' questions as he entered the police station.
Philadelphia prosecutors had decided not to charge him, but a judge acting on a private criminal complaint from a crash victim's family ordered misdemeanor charges filed.
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The case was referred to the state attorney general, who added a felony count of causing a catastrophe on top of eight misdemeanor counts of involuntary manslaughter and other charges.
The citizen complaint against Bostian was brought by attorneys for the family of Rachel Jacobs, a 39-year-old chief executive of a Philadelphia-based technology startup who was killed returning home to her husband and 2-year-old son in New York.
Just days before a two-year statute of limitations was to expire, Philadelphia prosecutors announced they had concluded there was insufficient evidence to prove that Bostian acted with intent or "conscious disregard" for the passengers' safety.
But victim lawyers said that should be an issue for a jury to decide.
Amtrak has taken responsibility for the crash and agreed to pay $265 million to settle claims filed by victims and their families.
The NTSB found no evidence that Bostian was impaired or using a cellphone. The agency also called Amtrak's long failure to implement automatic speed control throughout the busy Northeast Corridor a contributing factor.
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Bostian has a personal injury suit pending against Amtrak, saying he was left disoriented or unconscious when something struck his train before it derailed. He had heard through radio traffic that a nearby commuter train had been struck by a rock. However, the NTSB concluded that nothing struck his locomotive.
"The best we could come up with was that he was distracted from this radio conversation about the damaged train and forgot where he was," NTSB chairman Christopher Hart said at a May 2016 hearing.
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