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. 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.
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.
The sparse remains of Huanya Capac's royal estate and his country palace, called Quispiguanca, are in the Sacred Valley in the present-day town of Urubamba, Peru.
In present-day Bolivia, he was responsible for developing Cochabamba as an important agriculture and administrative center, with more than two thousand silos (qollas) for corn storage built in the area. Further north in Ecuador, Huayna Capac's forces attempted to expand into the lowlands of the Amazon basin, reaching the Chinchipe River, but they were pushed back by the Shuar.
The Inca empire reached the height of its size and power under his rule, stretching over much of present-day Bolivia, Peru, Argentina, Chile, Ecuador, and southwestern Colombia. It included varying terrain from high frozen Andes to the densest swamps, and more than two hundred distinct ethnic groups, each with their own customs and languages. The empire spanned 3,500 kilometres (2,200 mi) north to south comprising the Pacific Ocean coast on the west, the Andes, and extending to the Amazon Basin on the east.
Despite the geographical and cultural challenges, Inca or Tawantinsuyu, "the united four regions", was sophisticated for its time and place. At its height, it had monumental cities, temples, fortresses of stone marvelously engineered, roads cut through granite mountain slopes, and massive agricultural terraces and hydraulic works.
A dedicated ruler, Huayna Capac did much to improve the lives of his people. In addition to building temples and other works, Huayna greatly expanded the road network. He had storehouses (qollqas) built along it for food so that aid could be quickly rushed to any who were in danger of starvation.
Huayana knew of the Spanish arrival off the coast of his empire since 1515.
Huayna contracted a fever, perhaps from measles or smallpox upon returning to Quito, while campaigning in Colombia (though some historians dispute this). The Spaniards had carried smallpox to South America, and the Native Americans had not acquired immunity against it. Huayna and millions of other South and Central Americans died in that epidemic, including his brother, Auqui Tupac Inca, and successor eldest son, Ninan Cuyochi. Huayna Capac died in 1524,. His sons Atahualpa Inca and Huáscar Inca were granted two separate realms of the Inca Empire: his favorite Atahualpa, the northern portion centered on Quito, and his legitimate heir Huáscar, the southern portion centered on Cuzco. The two sons reigned peacefully for four to five years before Huascar Inca had second thoughts.
Huáscar quickly secured power in Cuzco and had his brother Atahualpa arrested. But Atahualpa escaped from his imprisonment with the help of his wife and began securing support from Huayna Capac's best generals Chalkuchimac and Quizquiz, who happened to be near Quito, the nearest major city. Atahualpa rebelled against his brother and won the ensuing civil war, imprisoning Huascar at the end of the war.
Pizarro and his men had the fortune of ascending into the Andes just as Atahualpa was returning to Cuzco after successful conclusion of his northern campaigns. After launching a surprise attack in Cajamarca and massacring upward of 6,000 Incan soldiers, Pizarro took Atahualpa prisoner. To secure his release, Atahualpa pledged to fill a room of approximately 88 cubic meters with precious golden objects, the famous Atahualpa's Ransom Room. Over the next months, trains of porters carted precious objects from across the empire, including jars, pots, vessels, and huge golden plates pried off the walls of the Sun Temple of Qurikancha in Cuzco. On May 3, 1533, Pizarro ordered the vast accumulation of golden objects melted down, a process that took many weeks. . Finally, on July 16, the melted loot was distributed among his men, and 10 days later, Pizarro had Atahualpa executed.
All the Inca emperors had their bodies mummified after death. Huanya Capac's mummy was on display in his palace in Cuzco and was viewed by the Spanish conquistadors of the Inca Empire. Later, it was taken from Cuzco to his royal estate of Quispiguanca where it was hidden from the Spanish by Huanya Capac's relatives and servants. At some point it was taken back to Cuzco, where it was discovered in 1559 by the Spanish. Along with mummies of 10 other Inca emperors and their wives, the mummy was taken to Lima where it was displayed in the San Andres Hospital. The mummies deteriorated in the damp climate of Lima and eventually they were either buried or destroyed by the Spanish.
An attempt to find the mummies of the Inca emperors beneath the San Andres hospital in 2001 was unsuccessful. The archaeologists found a crypt, but it was empty. Possibly the mummies had been removed when the building had been repaired after an earthquake.