The macabre discovery was made on a low bluff just a thousand feet from the Pacific Ocean, amid cinder block residential compounds in La Libertad outside Trujillo, Peru's third-largest city.
The 140 sacrificed children were five to 14 years old at the time of the ritualistic human sacrifice that cut their lives short.
Researchers also found footprints at the site suggesting the children were marched to their deaths.
Acknowledging that the discovery of human sacrifice has been found among the Aztec, Inca and Mayan cultures, Nat Geo noted that the Chimú find "is unprecedented in the Americas - if not the world".
Current research in Peru, officially called Huanchaquito-Las Llamas, conducted by an worldwide team funded by the National geographic society.
"They were possibly offering the gods the most important thing they had as a society, and the most important thing is children because they represent the future", said Gabriel Prieto, an archaeology professor at Peru's National University of Trujillo, who has led the excavation along with John Verano of Tulane University.
The discovery, by an worldwide team funded by the National Geographic Society, was made on Peru's northern coast at a site called Huanchaquito-Las Llamas.
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According to National Geographic, the children were "buried facing west, out to the sea".
All the skeletons showed signs of cuts to the sternum and rib dislocation, which points to the ancient sacrificial practice of heart removal, performed by cutting open the victims' chests.
Scientists first caught wind of the remains in 2011 when local residents told archaeologist Gabriel Prieto, a Huanchaquito native, human bones were showing up in the dunes near their home after the dunes eroded from the wind and the sea.
Peru's northern coast, where the children and baby llamas were found has been under excavation since 2011.
"I, for one, never expected it", Verano told the magazine of the sacrifice site, known to the researchers as "Las Llamas".
The remains of three adults - a man and two women - were also found near the mass grave of the children, with evidence of blunt force trauma on their skulls. The baby llamas were less than 18 months old. They had all apparently died of violent head wounds, and it is surmised they may have participated in the sacrifices. Radiocarbon dating pinpointed the date of the supposed sacrifice between 1400 and 1450. "It is ritual killing, and it's very systematic", Verano said. The layer could have been caused by the rains in the usually dry area - probably linked to extreme weather event such as the El Nino.
The researchers are now attempting to trace who the children were, and where they came from.