The remains, which dating from 2500 to 2900 BC, were buried in a way normally reserved for women of the Stone Age "Corded Ware" culture.
They were found in the Czech Republic, with the skull facing eastwards and surrounded by domestic jugs - rituals only previously seen in female graves.
Professor Kamila Vesinova, who led the dig, said that the caveman could even have been a transsexual.
"People from this period took funeral rites very seriously so it is highly unlikely this positioning was a mistake," he said.
"Far more likely is that he had a different sexual orientation, probably homosexual or transsexual."
In Corded Ware culture men were buried lying on their right side with their heads pointing west - alongside tools, weapons, food and drink. Women were buried on their left sides with jewellery and pottery.