21-year old Malik Layne is charged with murdering Tyreke Taylor after an argument spilled out of United Fried Chicken and Pizza.
Taylor left behind three children.
The incident happened on Adam Clayton Powell Boulevard and West 146th Street just before 1:15 a.m.
Authorities say the 35-year-old victim was shot in the neck and pronounced dead at the scene.
The gunman apparently got into a dispute with the victim inside the restaurant. Police say he then left, came back with the gun and opened fire.
Anguished family members rushed to the scene of the shooting.
They said the victim's brother was fatally shot in Harlem in June 2009, a crime that was never solved.
The restaurant opened last September.