Thick smoke filled the air near the Forest Hills MBTA station in Boston's Jamaica Plain neighborhood.
A fire inside a signal box led trains to grind to a halt.
The headaches were felt inside Back Bay Station.
"It's a little bit frustrating," said Carlos Aleman, who was supposed to leave for Washington at 8:15 a.m. He was still waiting at noon.
"Just tell us it's going to be closed for the day so I can go get some lunch, otherwise I'm here with all my stuff," he said.
Amtrak and commuter rail service suffered from big delays. Customer service ambassadors were brought in to help passengers.
"It could be 10 minutes, it could be an hour," said John Carlson, who was also delayed. "I don't know."
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The fire appears to have started inside a signal box. Keolis, the company that runs the commuter rail, says it appears the fire may have been caused by a lightning strike.
Radar shows a thunderstorm moving through Boston just before that fire broke out.
"The big challenge was determining is the power off, because it's unsafe to operate around a vault with that kind of power in it," said Boston Fire Deputy Chief Bernard Tully
Once firefighters were finally able to get close, they had to use special chemicals to help put out the fire. In the meantime, delays on Amtrak and the Stoughton/Providence commuter rail line are expected to last throughout the weekend.
