Police say the 21-year-old man was shot in a car while on the Cross Bronx Expressway service road just after 3:15 a.m.
He was shot in the abdomen and taken to Jacobi Medical Center, where he was listed in stable condition.
One of the other people in the car, believed to be the gunman, was taken into custody.
A weapon was recovered at the scene.
Police were looking for another person who fled on foot. They were also looking for another car that may be connected to the shooting.