Perhaps used in some sort of religious ritual or even for some sort of anicent medial school - or who knows?
They remain a mystery even today.
The ancient skulls carved out of crystal rocks were first discovered in South America as people were digging around in ancient ruins. Others crystal skulls were found elsewhere - even one was uncovered in Texas. Apparently who ever made them could journey around our planet in ancient times.
Needless to say - after the originals were found people made some modern duplications - which became hot collector items for a while.