Ithan Nick Ivan Tristly Tadin and another sibling with special needs were left under the care of their 35-year-old aunt when the fire broke out at about 7.30am.
It was learnt that the boy's father and grandparent had left the house at about 6am, as they rushed his expectant mother to the Tenom Hospital.
The boy's aunt and sibling were shocked to find their living room filled with thick smoke as they were having breakfast in the kitchen.
In her panic, the aunt managed to save the life of her special needs nephew but was not able to make it on time to save the four-year-old who was in another room.
District Fire and Rescue Department Chief, Runzee @ Syamree Abdul Thani, said they received a call at about 7.44am and two fire engines manned by 13 personnel reached the scene at about 8.07am.
The operation ended at about 9.30am and the Fire and Rescue Forensic Unit is investigating the cause of the fire.
District Police Chief DSP Mohd Firdaus Abdullah said there were no elements of foul play and classified the case as sudden death.
Rural Development Minister Datuk Radin Malleh visited the family and donated an undisclosed amount to the boy's grandfather, Tadin Surangking, who is attached to a government department.