The Inca Empire did not have a single emperor at a time, but seem to have always embraced the Moche ideal of duality. There were two Inca rulers, one from the Hanan and one from the Hurin that each had their own section of Cuzco. The Hanan was on higher ground and the time of the conquest the Hanan ruler was the Supa Inca, or Unique Inca. The post conquest chronicalers were obsessed with the mediaeval concept of legitimate hereditary rule, and only recorded the names of the Supa Inca and their "queens".

The Supa Inca of the first dynasty of the Kingdom of Cuzco were, in order: Manco Capac (– 1105 CE), Sinchi Roca (1105 CE – 1140 CE), Lloque Yupanqui, Mayta Capac, and Capac Yupanqui. We do not know much about these early rulers. As a rough guide in later years capac meant warlord, and sinchi meant leader.

The Supa Inca of the second dynasty of the Kingdom of Cuzco were, in order: Inca Roca, Yahuar Huacac, Viracocha, and Pachacuti. The second dynasty marked the transition in dominance from the Hurin to Hanan family.

The first Supa Inca of the Tahuantinsuyu, or Inca empire, was Pachacuti (1438 CE – 1471 CE), he was followed by Tupac Inca Yupanqui (1471 CE – 1493 CE), Huayna Capac (1493 CE – 1527 CE), Ninan Cuyochi* (1527 CE), Huascar (1527 CE – 1532 CE), and, finally, Atahualpa (1532 CE – 1533 CE). Pachacuti reorganized the empire into gour suyus each governed by an Apo, with several layers of administration below him. He also adopted the Chimú custom of split-inheritance. Under this system one potential heir would receive the political inheritance, while the property and water rights of the the previous Inca would be split between the other potential heirs. This sated the other potential heirs materially, and encouraged the new Inca to conquer new territory so that he would have some property.

After the conquest of by the Spanish, there were several more Inca who led the government in exile. They were: Tupac Huallpa (1533 CE), Manco Inca Yupanqui (1533 CE – 1545 CE), Sayri Tupac (1545 CE – 1560 CE), Titu Cusi (1560 CE – 1571 CE), and, most famously, Tupac Amarú.

* Ninan Cuyochi is sometimes left off the list because news of his death from smallpox arrived in Cuzco shortly after he was declared Supa Inca. But he was the Inca if even only for a day or two. He had been with Huayna Capac when he died of smallpox. The death of Ninan, the presumed heir, led to a civil war between Hualpa Huascar and Atahualpa.