A switching problem was blamed for the shutdown that began at 5:20 p.m. EST, The New York Times reported. Limited service resumed just before 7 p.m., officials said.
The electrical problem affected all trains, including Amtrak, New Jersey Transit and Long Island Rail Road.
Long Island Rail Road spokesman Sal Arena said the electrical problem "affected a switch or switches right at the point where trains leave or enter Penn."
During the stoppage, police were not letting people into the station but didn't force those inside to leave, he said.
Because there had been extra trains running during the pre-holiday afternoon, Arena said, "we may not have as many people in Penn Station as we do on a typical Wednesday night."
"That said, they're still not going anywhere," he added.