He died of smallpox shortly before or after the death of his father, also reportedly from smallpox, bringing about the Inca Civil War in which Huáscar and Atahualpa fought to be the next Sapa Inca.
[1] According to writer Burr Cartwright Brundage, Ninan Cuyochi had a strong faction when Inti's high priest in Quito prepared to confirm his candidacy as next Sapa Inca in 1527.
Thus, although Huayna Capac named the infant Ninan Cuyochi as his first heir, sources differ as to whether the boy died first, was unacceptable because of an unfavorable divination, or even if Huayna simply forgot that he had named him when asked to confirm the nomination.
[3] Regardless, after Huayna Capac's and Ninan Cuyochi's death, Huáscar took on the royal fringe.
The dispute over this led to civil war between Huáscar and Atahualpa, the latter of whom was backed by leaders who were based in the north.