The subway may be shuttered nightly for the duration of the coronavirus pandemic, but near-empty “ghost trains” continue to run during shutdown hours.

Trains will continue to run between 1 a.m. and 5 a.m., carrying transit workers and cops when necessary, a senior MTA source told The Post.

That explains why New Yorkers passing over and under subway tracks Wednesday morning may have been surprised to hear the hum of trains coming from the transit system.

Transit officials opted to keep trains running because of a lack of space to store trains elsewhere at once, and the need to position trains for the 5 a.m. morning rush, the senior source said.

Additionally, the MTA uses the mostly-empty trains to monitor for fires and other unsafe conditions, such as people walking tunnels, according to the source.

Running mostly-empty trains back and forth is standard practice for strikes and weather events, a former transit official told The Post in March.

“Generally, all of the shutdown scenarios that we’ve had included trains running on the tracks without passengers,” the former staff said.

“The building’s not completely empty, so to speak.”

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