Kaguya Ōtsutsuki was the first human to possess chakra and is the mother of the Sage of the Six Paths.
Background
During one of the wars of old, Kaguya took and ate one of the forbidden fruits of the God Tree. Afterwards, she gained the ability to use chakra and used it to end the war all on her own.
Sometime afterwards, she had her son, who was naturally born with chakra.