The exact date of Huayna Capac's birth is unknown; it may have been in 1468, most probably in Tumebamba (modern Cuenca) where he also may have spent part of his childhood. He was the son of Topa Inca. Topa Inca (ruled 1471-1493) had extended Inca rule north into present-day Ecuador, a process continued by Huayna Capac.
Huayna Capac's legitimate wife and full sister was Coya Cusirimay. The couple produced no male heirs, but Huayna Capac sired more than 50 sons with other women. Huayna Capac took another sister, Araua Ocllo, as his royal wife; they had a son called Tupac Cusi Hualpa, also known as Huáscar. Other children included Ninan Cuyochi, Atahualpa, Túpac Huallpa, Manco Inca Yupanqui, General Atoc, Paullu Inca, and Quispe Sisa.:112,118 Many of them later once held the title of Sapa Inca, although some were installed by the Spaniards.
Since he was a "boy chief" or "boy sovereign", he had a tutor, Hualpya, nephew of Inca Yupanqui. This tutor's plot to assume the Incaship, was discovered by the Governor Huaman Achachi, who had Hualpya killed.:109
Huayna Capac extended the Tawantinsuyu (Inca Empire) significantly to the south into present-day Chile and Argentina and tried to annex territories towards the north, in what is now Ecuador and southern Colombia.
In Ecuador, formerly known as the Kingdom of Quito, Huayna Capac absorbed the Quito Confederation into the Inca Empire after marrying the Quito Queen Paccha Duchicela Shyris XVI in order to halt a long protracted war. From this marriage Atahualpa was born (1502 AD) in Caranqui, Ecuador. Atahualpa was to inherit the Kingdom of Quito, by the will of his father Huayna Capac, and later Inca Emperor after defeating his brother, the Inca Emperor Huascar in the Inca Civil War, where the Inca Huascar attempted to conquer the Kingdom of Quito after 7 years of peace. Huayna Capac spent most of his time in Ecuador which he became fond of and as a result founded cities like Atuntaqui. The capital city of the Tawantinsuyu was in Cuzco and rebuilt Quito making it the second capital of the Inca Empire. Huayna Capac built astronomical observatories in Ecuador such as Ingapirca. Moreover, Huayna Capac hoped to establish a northern stronghold in the city of Tumebamba, Ecuador where the Cañari people lived.