The boy was left in the care of a babysitter inside a New York Avenue apartment in the Crown Heights section on Sunday.
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The child's identity has not yet been released.
He was rushed to Kings County Hospital with head and neck trauma just before 9:45 p.m.
A 29-year-old relative of the boy's babysitter is being questioned in his death. No charges were immediately filed.
The boy's mother initially asked a 54-year-old family friend to watch the boy. That man's younger relative is believed to have been with the child when he suffered head and neck trauma.
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The medical examiner will determine the boy's cause of death.
The investigation is ongoing.
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