"The child's body was burnt completely 5,000 years ago," said Farzad Forouzanfar, an anthropologist from the Burnt City archeological team, on Wednesday.
"The skeleton was found in the 12th phase of Burnt City archeological excavations," he added.
According to Forouzanfar, only the skull and a part of the child's face had survived the fire.
"The child's limbs were in a normal position, which means that the child didn't move during the fire," press tv quoted him as saying.
Evidence shows that the child had been suffocated by carbon monoxide before he was burnt.
Earlier in the 12th phase, 52 skeletons and 12 ancient graves, believed to be unique among the discoveries of the past 30 years, were also found.
Over 400 prehistoric sites have been excavated in Burnt City and archeologists expect the number to reach 1,000.
The 5,000-year-old Burnt City is located near the city of Zabol and spans an area over 300,000 square hectares.
Four civilizations have lived in the city, which burned down three times and was not rebuilt after the last fire.
The world's oldest dice and backgammon set, the earliest known caraway seed and an artificial eyeball are some of the recoveries of the Burnt City.