The NYPD said 16-year-old Tajay Richards is facing multiple charges, including attempted murder, assault, and criminal possession of a weapon.
A 27-year-old man had been arrested previously, but police later determined he was not the gunman and not involved in the dispute that led to the shooting.
The NYPD continues to search for more people who are wanted for questioning in the case.
The shooting happened February 26 at Flatlands Avenue between East 82nd and East 83rd Street in the Canarsie section.
Police say two groups of individuals were involved in a dispute that spilled out into the street. The argument began inside a Popeye's fast food restaurant.
One of them fired several rounds at members of the opposing group.
One of the stray bullets entered a van that had pulled up to a red light and pierced the window behind the driver's seat where the girl was sitting. A bullet fragment struck her in the back of the head.
The girl was taken to Brookdale Hospital in serious but stable condition but is now recovering at home.
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