The case was referred to the office of Attorney General Josh Shapiro, who can either decide to comply with the order and charge Bostian or appeal it to the state Superior Court.
Eight people died and more than 200 were injured in the crash.
But Philadelphia Municipal Court President Judge Marsha Neifield ordered the district attorney to charge Bostian at the urging of attorneys representing dozens of the victims.
Each misdemeanor charges carries a maximum five-year sentence.
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.
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However, it could be entirely possible this was the focus of the producers because it allowed for extraordinary special effects. He said: "The guy that looked after them said I would probably get one presented to me at the wrap party".
"It's a moment of bringing a man to task for what he did to all these families and how he did this so wrong", said Thomas R. Kline, the attorney for the victims' families. Bostian was an experienced engineer.
Mr. Mongeluzzi added, "The Attorney General's bold, decisive action sends a loud and clear message that endangering the lives of rail passengers, crews and the public will not be tolerated in Pennsylvania, and should not be tolerated anywhere", said Mr. Mongeluzzi.
Investigators found that the train was travelling at 106mph (170km/h) along a curve - more than double the speed limit for that section of the line.
After he "lost situational awareness as to where his train was located in relation to the curve", the NTSB said, Mr Bostian actually accelerated the train to past 100mph - "consistent with a belief that his train had already passed the curve into an area of relatively straight track". He had become aware, through radio traffic, that a nearby commuter train had been struck by a rock. The automated system notifies an engineer if the train is speeding and applies the brakes automatically if the engineer does not respond.
Other lawyers have called last year's NTSB report on the crash a "whitewash" and a "quantum leap".
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They're 6-0 here during the playoffs, but to advance to the conference finals they'll have to win at TD Garden. To win Game 7, the Wizards would prefer it doesn't come down to such a finish on the road.
"Yet prosecutors say they have 'no evidence that the engineer acted with criminal "intent" or criminal "knowledge", ' and they do not believe there's enough evidence to prove that Bostian acted with 'criminal recklessness'".
As NPR's Merrit Kennedy reported in October, a federal judge approved a $265 million settlement between Amtrak and people affected by the crash.
Bostian suffered a blow to the head in the crash, which his lawyer said affected his memory of the event.
The move comes days after prosecutors in the city of Philadelphia said they would not pursue charges. Jacobs, a technology executive, was a wife and mother. The other people killed included Justin Zemser, a Naval Academy midshipman; Jim Gaines, an Associated Press software architect; and Derrick Griffith, a college dean.
Global ransomware attack based on stolen NSA tools cripples computer networks worldwide
Hospitals, with their often outdated IT systems and trove of confidential patient data, are a particularly tempting target. The cyberattack forced hospitals to divert emergency patients and locked doctors and other staff out of their computers.
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