The Inca people were a pastoral tribe in the Cusco area around the 12th century. Peruvian oral history tells an origin story of three caves. The center cave at Tampu T'uqu (Tambo Tocco) was named Qhapaq T'uqu ("principal niche", also spelled Capac Tocco). The other caves were Maras T'uqu (Maras Tocco) and Sutiq T'uqu (Sutic Tocco). Four brothers and four sisters stepped out of the middle cave. They were: Ayar Manco, Ayar Cachi, Ayar Awqa (Ayar Auca) and Ayar Uchu; and Mama Ocllo, Mama Raua, Mama Huaco and Mama Qura (Mama Cora). Out of the side caves came the people who were to be the ancestors of all the Inca clans.

The Inca, led by Manco Capac(leader of the ayllu, a nomadic tribe), migrate to the Cuzco Valley and establish their capital at Cuzco. Upon arriving to the Cusco valley, they defeated three small tribes that lived there; the Sahuares, Huallas and Alcahuisas, and then settled in a swampy area between two small streams, that today corresponds with the main plaza of the city of Cusco. Manco Capac oversees the construction and development of the Kingdom of Cusco, initially a small city-state. Archaeologist John Rowe calculates 1200 AD as an approximate date for the founding of the Inca dynasty — long before the foundation of the empire.

For approximately 200 years, the Incas remain settled in Cusco and its surrounding area. According to Gordon Francis McEwan, “Between A.D. 1200 and 1438 eight Incas ruled without the Incas expanding much outside their heartland in Cusco.”

Sinchi Roca is said to have created a territorial division of his domains and is considered to be the initiator of the first census of the Inca population. He also ordered all members of his ethnic group (Inca) to pierce their ears as a sign of nobility. He solidifies Inca power in Cusco by creating an army composed of soldiers who belonged to the nobility cast. Sinchi Roca dresses his soldiers in uniform which intimidated his enemies. The chronicler Pedro Cieza de León states that Sinchi Roca built terraces and credited with bringing great quantity of soil to improve the fertility of the valley and of building the first water canal in the Huatanay and Tullumayo rivers.

Lloque Yupanqui was the son and successor of Sinchi Roca. Although some chronicles attributed minor conquests to him, others say that he did not wage any wars, or that he was even occupied with rebellions. He is said to have established the public market in Cuzco and built the Acllahuasi. In the days of the Inca Empire, this institution gathered young women from across the empire; some were given by the Inca as concubines to nobles and warriors and others were dedicated to the cult of the Sun god. Sometimes they were simply servants.

Mayta Cápac (Quechua Mayta Qhapaq Inka) was the fourth Sapa Inca of the Kingdom of Cuzco, He was referred to as the reformer of the calendar. The chroniclers describe him as a great warrior who conquered territories as far as Lake Titicaca, Arequipa, and Potosí. While in fact, his kingdom was still limited to the valley of Cuzco. Mayta Cápac put the regions of Arequipa and Moquegua under the control of the Inca empire. His great military feat was the subjugation of Alcabisas and Culunchimas tribes.

Yupanqui was a son and successor of Mayta Cápac while his elder brother Cunti Mayta became high priest. In legend, Yupanqui is a great conqueror; the chronicler Juan de Betanzos says that he was the first Inca to conquer territory outside the valley of Cuzco—which may be taken to delimit the importance of his predecessors. He subjugated the Cuyumarca and Ancasmarca. Garcilaso de la Vega reports that he improved the city of Cuzco with many buildings, bridges, roads and aqueducts.

Inca Roca (Quechua Inka Roq'a, "magnanimous Inca") was the sixth Sapa Inca of the Kingdom of Cusco (beginning around CE 1350) and the first of the Hanan ("upper") Qusqu dynasty. After Cápac Yupanquiʻs death, the hanan moiety rebelled against the hurin, killed Quispe Yupanqui, and gave the throne to Inca Roca, son of another of Cápac Yupanquiʻs wives, Cusi Chimbo. Inca Roca moved his palace into the hurin section of Cuzco. In legend, he is said to have conquered the Chancas (among other peoples), as well as established the yachaywasi, schools for teaching nobles. More soberly, he seems to have improved the irrigation works of Cuzco and neighboring areas, but the Chancas continued to trouble his successors. (He creates yachaiwasis or schools for the nobles. Under his reign he establishes friendly ties with nearby tribes).

Yawar Waqaq or Yawar Waqaq Inka was the seventh Sapa Inca of the Kingdom of Cusco (beginning around CE 1380) and the second of the Hanan dynasty. His father was Inca Roca (Inka Ruq'a). Yawar's wife was Mama Chicya (or Chu-Ya) and their sons were Paucar Ayllu and Pahuac Hualpa Mayta. As a child he was kidnapped by the Ayarmacas because of a marital conflict. He eventually escaped with the help of one of his captor's mistresses, Chimpu Orma. Assuming the reign at the age of 19, Yawar conquered Pillauya, Choyca, Yuco, Chillincay, Taocamarca and Cavinas. Yahuar Huaca is not very healthy and spends most of his time in Cusco. He appoints his second son Pahuac Gualpa Mayta as his successor but is killed by one of his concubines who wanted her son to be the Sapa Inca. Yahuar Huaca is also assassinated along with his other sons.

Viracocha (in hispanicized spelling) or Wiraqucha (Quechua, the name of a god) was the eighth Sapa Inca of the Kingdom of Cusco (beginning around 1410) and the third of the Hanan dynasty. He was not the son of Yawar Waqaq; however, it was presented as such because he belonged to the same dynasty as his predecessor: the Hanan.

The Chanca (or Chanka) tribe, a “powerful warlike confederation” (McEwan), attacks the city of Cusco as it attempts an aggressive expansion to the south. Pachacuti led the military defense against the Chanka while his father and his brother, Urco Inca, fled the manor. The victory over the Chankas made Inca Viracocha recognize him as his successor around 1438. He conquered the provinces of Colla-Suyu and Chinchay-Suyu. Along with his sons, Tupac Ayar Manco (or Amaru Tupac Inca), and Apu Paucar Usnu, he defeated the Collas. Additionally, he left garrisons in subjugated lands. Pachacuti rebuilt much of Cusco, designing it to serve the needs of an imperial city and as a representation of the empire. Most archaeologists now believe that the famous Inca site of Machu Picchu was built as an estate for Pachacuti.

The Battle of the Maule was fought between a coalition of Mapuche people of Chile and the Inca Empire of Peru. The account of Garcilaso de la Vega depicts the three-day battle, which is generally believed to have occurred in the reign of Tupac Inca Yupanqui (1471-93 CE). Arguably the Inca's advances in Chile were halted by their unwillingness to commit greater resources in fighting the Mapuche. There are conflicting arguments between sources for the specific date, location, causes, etc for this battle.

Huayna Capac dies, possibly from smallpox (an epidemic had been tearing through the New World immediately after its introduction by the Spanish). Catastrophically, Huayna Capac had failed to name an heir before his death. The ensuing power struggle between his two sons, Huáscar and Atahualpa, eventually leads to a civil war. Huascar assumes the throne supported by the nobility in Cusco. Meanwhile Atahualpa, who was considered a more capable administrator and warrior, is crowned Sapa Inca in Quito. It is unknown how many Inca were killed or died during the civil war. The estimated population of the Inca empire before an epidemic (probably of a European disease) and the Spanish conquest is estimated at between 6 and 14 million people. The civil war, an epidemic, and the Spanish conquest resulted in a population decline over several decades estimated as 20:1 or 25:1, meaning that the population declined by 95 percent.

The Battle of Cajamarca also spelled Cajamalca was the ambush and seizure of the Inca ruler Atahualpa by a small Spanish force led by Francisco Pizarro, on November 16, 1532. The Spanish killed thousands of Atahualpa's counselors, commanders, and unarmed attendants in the great plaza of Cajamarca, and caused his armed host outside the town to flee. The capture of Atahualpa marked the opening stage of the conquest of the pre-Columbian civilization of Peru.

Atahualpa offered the Spaniards enough gold to fill the room he was imprisoned in and twice that amount of silver. The Inca fulfilled this ransom, but Pizarro deceived them, refusing to release the Inca afterwards. During Atahualpa's imprisonment Huáscar was assassinated elsewhere. The Spaniards maintained that this was at Atahualpa's orders; this was used as one of the charges against Atahualpa when the Spaniards finally executed him, in August 1533. In accordance with his request, he was executed by strangling with a garrote on 26 July 1533. His clothes and some of his skin were burned, and his remains were given a Christian burial.

In August 1536, some 50,000 warriors marched on Lima under the command of Manco Inca’s most valiant general, Quizo Yupanqui, with orders to kill every Spaniard in the newly founded capital. The siege failed and Quizo, the Inca general died, and the Inca army retreated. Francisco Pizzarro would mount a relief of the Siege of Cuzco.

The Battle of Ollantaytambo took place in January 1537, between the forces of Inca emperor Manco Inca and a Spanish expedition led by Hernando Pizarro during the Spanish conquest of Peru. To end the stand-off, the besieged mounted a raid against the emperor's headquarters in the town of Ollantaytambo. The expedition, commanded by Hernando Pizarro, included 100 Spaniards and some 30,000 Indian auxiliaries against an Inca army more than 30,000 strong.

After the fall of the Inca Empire many aspects of Inca culture were systematically destroyed, including their sophisticated farming system, known as the vertical archipelago model of agriculture. Spanish colonial officials used the Inca mita corvée labor system for colonial aims, sometimes brutally. One member of each family was forced to work in the gold and silver mines, the foremost of which was the titanic silver mine at Potosí. When a family member died, which would usually happen within a year or two, the family was required to send a replacement.

The effects of smallpox on the Inca empire were even more devastating. Beginning in Colombia, smallpox spread rapidly before the Spanish invaders first arrived in the empire. The spread was probably aided by the efficient Inca road system. Smallpox was only the first epidemic. Other diseases, including a probable Typhus outbreak in 1546, influenza and smallpox together in 1558, smallpox again in 1589, diphtheria in 1614, and measles in 1618, all ravaged the Inca people.

There would be periodic attempts by indigenous leaders to expel the Spanish colonists and re-create the Inca Empire until the late 18th century.