The worker was struck by a Metro North train traveling from Grand Central to New Haven, officials said.
The man's identity was not immediately released. Power was turned off to all four tracks to allow emergency personnel to reach the scene.
Metro North spokeswoman Marjorie Anders said at least a dozen New Haven line trains were held at the nearest stations, affecting an estimated 12,000 commuters.
Some service resumed on the New Haven line through Rye after 8:30 p.m. Metro North was able to clear one of the four tracks. It was handling train traffic in both directions, but New Haven-bound trains were getting the priority considering rush hour service was affected. Delays of up to one hour were expected.
Five Amtrak trains between New York and New Haven were halted as well.
Passengers waiting at Penn Station in Manhattan were not given any timetable. The departure board still read "delayed" for trains due to depart at 8:00 p.m.
People waiting to pick up family or friends learned by cell phone calls from them that at least one train was moving toward the city around 10:30 p.m.
Minutes later, an announcer said train 175 from Boston to Washington would arrive around 11:00 p.m. The delayed trains arrived between 11 and 11:30 p.m.
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