The criminal complaint was filed by Pennsylvania's top prosecutor just three days after Philadelphia's district attorney decided not to file charges against Bostian in the crash of Amtrak Northeast Regional Train 188.
Brandon Bostian has been charged with involuntary manslaughter, causing or risking a catastrophe, and "numerous" counts of reckless endangerment, prosecutors said.
Amtrak train 188 was on its way from Washington to NY on 12 May 2015 when it came off the track in the city of Philadelphia.
"I commend our outstanding team in the office of the Attorney General, (which) worked diligently and thoughtfully around the clock to enable us to be in this position to pursue justice on behalf of the victims of this deadly crash", Shapiro said. Eight passengers died and more than 200 were injured in that preventable catastrophe.
Philadelphia prosecutors announced earlier in the week that they couldn't prove Bostian acted with "conscious disregard" when he accelerated the train to 106 miles per hour on a curved stretch of track where the speed limit was 50 miles per hour.
The family of a NY woman who was killed sought the criminal complaint after city prosecutors declined to press charges.
He is expected to surrender to make a court appearance but that will not likely happen Friday night, officials said.
The judge's unusual order came a day before Friday's two-year deadline to file charges in the May 12, 2015, crash that killed eight. Citing a conflict, the DA referred the case and charging decision to the Attorney General. Bostian's lawyer has rarely commented and did not return messages seeking comment this week.
Amtrak has taken responsibility for the crash and agreed to pay $265 million to settle related claims. Jacobs, a technology executive, was a wife and mother.
Bostian has a personal injury lawsuit pending against Amtrak.
"We have no evidence that the engineer acted with criminal "intent" or criminal 'knowledge", prosecutors said in a statement at the time. He said he was left disoriented or unconscious when something struck his train before it derailed.
Attorneys Thomas Kline, left, Richard Sprague and Robert Mongeluzzi take part in a news conference while standing next to a photo of train engineer Brandon Bostian in Philadelphia on Thursday. He had become aware, through radio traffic, that a nearby commuter train had been struck by a rock. Per Pennsylvania law, involuntary manslaughter when it was a direct result of reckless or negligent behavior is a first-degree misdemeanor punishable by two-and-a-half to five years in prison per charge. However, the National Transportation Safety Board concluded that nothing struck his locomotive.