Officers were called to the scene in Hunts Point just after 4:00 Sunday morning.
The victim apparently ran to a gas station directly below the station at Bruckner Boulevard on the 6 line.
He was shot in the foot, police said, and taken to Montefiore Hospital for treatment.
A getaway car was found about a mile away from the scene, but so far, no arrests.
Service on the 6 line experienced minor delays because of the investigation.
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