The southbound train caught fire on the express tracks at the station just before 2:30 a.m.
Heavy smoke spewed from the station as commuters who were waiting on the platform fled to the street.
The train is a vacuum train, used to clean up debris and litter off the tracks to prevent fires and delays.
The incident has led to service disruptions on the 4 and 6 trains. For service between Grand Central-42 St and Brooklyn Bridge-City Hall, consider the M15, M102, or M103 bus.
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