Last week, police say they pepper sprayed 19-year-old Shamel Jones when he charged at them in the Longwood section of the Bronx.
He then continued towards them, prompting the officers to open fire.
Jones was hit in the lower back.
He has now been charged with assault, menacing, criminal possession of a weapon, and criminal mischief.
Police had received a call from the girlfriend of Jones, saying he had assaulted her.
Officers showed up to find her with several bruises to the eye and face area, and when they arrived, they saw Jones flee the scene.
He was located a few doors down in an apartment building, inside a bedroom.