Four-year-old Christopher Alfaro Rodriguez died from smoke inhalation in the fire back in March.
Investigators said his mother Alianny Rodriguez initially told officers she had briefly left to get food before returning to find the home on fire.
But they said evidence later showed she had been away from the house for nearly 20 hours, leaving the child alone.
Rodriguez was charged with involuntary manslaughter, child endangerment causing death and child abandonment.