Train disruptions persisted into the Thursday evening rush after a morning fire in an East River tunnel upended service in and out of Penn Station.

Amtrak spokesperson Jason Abrams said the blaze broke out at 11:25 a.m. in a tunnel that connects the Long Island Rail Road between Manhattan and Queens. He said the fire wasn’t put out until 12:55 p.m.

The MTA halted Long Island Rail Road service in both directions between the train hub and Jamaica Station, and NJ Transit diverted all its Midtown Direct transit to Hoboken Terminal. The service disruptions persisted after the fire was put out.

The MTA directed LIRR riders to head to Atlantic Terminal or Grand Central Madison to get home. The agency said they'd cross-honor their LIRR tickets on the subway. Several NJ Transit trains were either delayed or canceled outright.

Crowds of outraged riders huddled near platform entrances, and many were confused by the outages.

"The one day I come into the city there's a fire and there's a delay," said West Hempstead resident Pollyanna McFarlane, 64, who uses a cane and said she did not want to take the subway. "This is why I usually do not take jobs in the city. My jobs in the last couple years have been on Long Island, where I could comfortably get in my car and drive to my job."

Commutes out of Penn Station were hellish after a track fire upended service at the country's busiest train station.

Jamaica Station was hardly any better, as crowds scurried to figure out which train to take home while LIRR crews tried to improvise new timetables. Riders boarded on a Huntington-bound train after 5 p.m., only to learn it had been canceled and they'd have to deboard.

The FDNY said there were no injuries from the track fire, and officials were investigating its cause.

The MTA blamed the problem on Amtrak, which owns the tracks and the tunnels at Penn Station. It comes as Amtrak has shut down one of its East River Tunnels for repairs, limiting the LIRR’s ability to redirect trains during emergencies.

Amtrak reported just before 2 p.m. the fire had been extinguished, and that its service was also suffering from delays.

The delays landed two days before LIRR workers prepared to go on strike, which would shut down the railroad.

Sean Bowditch contributed reporting to this story.