The 6-year-old boy and his 2-year-old sister were both slashed by their mother, 24-year-old Shanice Martin on April 27.
The injuries were serious: The boy's neck had been slashed ear-to-ear and he underwent surgery.
After the incident, Martin walked into the NYPD's 42nd Precinct covered in blood and told police what had happened.
She was arrested, charged and is undergoing a psychiatric evaluation.
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Police sources said the child had since returned to school, but collapsed around 11:30 a.m.
He was taken to a local hospital, where he was pronounced dead.
Authorities have not confirmed whether or not the child died as a result of his previous slashing injuries. An investigation is ongoing.
Martin's family said she was living in and out of shelters with her two kids and was upset when she could not get into one. She called her mother, but then an hour later, NYPD officers found the two children in the street with slash wounds.
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"She was a good mom, but I guess she was going through something," Martin's brother, Travone Lango, said after the slashing. "That's not something that you do to your kids. I don't care what's going on with you, you can ask for help. She just took it upon herself to do what she wanted to do, and it's not good."
She was arrested and charged with assault, child abandonment, endangering the welfare of a child and criminal possession of a weapon.
In response to Friday's tragedy, Schools Chancellor Richard Carranza released a statement: "I'm heartbroken by this tragic loss of a student, and my thoughts are with the family and school community. We are working in partnership with City agencies as they investigate, and are providing additional guidance counselors and support to the school for as long as needed."