At 10:50 Wednesday morning, officers responded to a 911 call from the Ritz Plaza apartment building at 235 West 48th Street, where the boy's babysitter lives.
They found the boy unconscious and unresponsive.
EMS responded and transported the child to Roosevelt Hospital where he was pronounced dead.
The Medical Examiner will determine the cause of death and the investigation is ongoing.
The boy's identity has not yet been released.
The boy's 37-year old caregiver told police she had put the child on the bathroom counter and left the room briefly. Police say the woman told them that the boy fell off the counter and landed in the empty bathtub.
But detectives say he had cuts and third-degree burns on his body, including cigarette burns.