The assault happened on the platform of the Franklin Avenue shuttle in Crown Heights, police said.
Jovan Frederick, 32, faces attempted murder, assault and robbery charges, police said.
The victim is being treated at Kings County Hospital after Friday morning's attack in Crown Heights.
The victim in the Dec. 18 shooting was not the intended target, police said.
A recent fight between two gang-affiliated groups fueled an uptick in shootings, officials said.
Police believe the victim was not the intended target of the Thursday afternoon shooting.
The assault happened near the Prospect Park stop on the B/Q line, police said.
The shooting was one of three that occurred within 12 hours in the neighborhood Tuesday and Wednesday.
Police Commissioner Bill Bratton said Tuesday there is "no specific credible threat" to New York.
A man targeting older people has struck three times in two weeks in Crown Heights, police said.
While the Oct. 11 incident was not classified a hate crime, a hate crimes detective is aiding the case.
The graffiti was found a week after a Jewish tenant moved into the President Street apartment building.
The latest assault came just a day after a 24-year-old Jewish man was punched in the face, police said.
Jadeocus Muhammad was turned himself in Monday for trying a rape a woman early Saturday, police said.
The incident took place at a bodega at the corner of Utica Avenue and Eastern Parkway.
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