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Representation of the Sapa Inca (Pachacutec) wearing a "maskaypacha real" (royal badge), in the main square of Aguas Calientes, Peru.

The God Emperor of the Inca Empire (quechua: Inka Qhapaq) of the Andes (the area including modern Peru, Ecuador, and Bolivia) used the titles Sapa Inka ("the only Inca"), Sapa ("the only one"), and Apu ("divinity").

Leadership systems at all levels within the Inca Empire were structured by moieties entitled the Hanan (upper) and the Hurin (lower), in keeping with the ideal of duality. The leaders of the two moieties ruled together and were ranked equally, although the hanan leader had greater prestige and therefore dominance. At the time of the Spanish conquest of Peru the supreme leader of the empire of the Hanan moiety was called the Sapa Inca. This concept of duality was lost to the Spanish, whose post-conquest chroniclers only recorded the names of the Sapa Inca, the empire's hanan ruler at the time, and his "queens", and left off the Hurin.

The Sapa Inca of the first dynasty of the Kingdom of Cuzco were, in order, Manco Capac, Sinchi Roca, Lloque Yupanqui, Mayta Capac, and Capac Yupanqui. Little is known of these early rulers, but as a rough guide, in later years capac meant warlord and sinchi meant leader. The beginning of the dynasty is generally taken as about 1200 CE.

The Sapa 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 Sapa Inca of the Tawantin Suyu, or Inca empire, was Pachacuti (1438-1471). He was followed by Tupac Inca Yupanqui (1471-1493), Huayna Capac (1493-1527), Ninan Cuyochi (?-1527), Huascar (1527-1532), and, finally, Atahualpa (1532-1533).

Pachacuti reorganized the empire into four suyus (provinces), 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 property and water rights would be split between the other potential heirs. This sated the other potential heirs materially and encouraged the new Inca to conquer new territory to acquire property.

Ninan Cuyochi, who was Inca for only a few days, is sometimes left off the list of Sapa Incas because news of his death from smallpox arrived in Cuzco shortly after he was declared Sapa Inca. He had been with Huayna Capac when he died of smallpox. The death of Ninan, the presumed heir, led to a war of succession between Huascar and Atahualpa, a weakness that the Spanish exploited when they conquered the Incas.

After the conquest, there were several more Sapa Incas before the Inca leadership system dissolved completely. They were Tupac Huallpa (1533), Manco Inca Yupanqui (1533-1545), Sayri Tupaq (1545-1560), Titu Cusi (1560-1571), and, finally, Tupac Amaru. This last Sapa Inca must not be confused with Tupac Amaru II, leader of an eighteenth-century Peruvian uprising.