The boy's DNA, which is the oldest nuclear genome to be sequenced, shows close ties to today's Native Americans.
This finding traces a third of their ancestry to "western Eurasia" with the other two thirds coming from eastern Asia, said DNA expert and study author Eske Willerslev of the University of Copenhagen.
This also implies that traces of European ancestry previously detected in modern Native Americans did not come solely from mixing with European colonists, as most scientists had assumed previously.
While most researchers agree that the first Paleoamericans moved across the Bering Land Bridge some 15,000 years ago, they have always debated their ancestry. But previously found skeletons which dated back to 9,000 years ago and had European features led the study's authors to consider a European ancestry.
The DNA sample comes from the right hand of the boy who lived near Siberia's Belaya River in a village called Mal'ta. His grave was adorned with flint tools, pendants, a bead necklace, and a sprinkling of ochre.
One expected relation that was missing was the boy's genome had no connection to modern Asians. While the majority of Native American ancestry show East Asian origins this was missing from the boy's genome. But Willerslev said that this does not take away from the validity of the research.
The researchers propose that before 24,000 years ago, the ancestors of Native Americans split into two groups, with the boy's group moving east into Siberia from Europe and West Asia. In this scenario, that group then intermixed with East Asians before moving on to North America.
"Mal'ta might be a missing link, a representative of the Asian population that admixed both into Europeans and Native Americans," said Harvard geneticist David Reich. If so, he said, it shows "the value of ancient DNA in peeling back history and resolving mysteries that are difficult to solve using only present day samples."