Túpac Amaru II was born José Gabriel Condorcanqui Noguera between March 8 and 24, 1738 in Surimana, Tungasuca, in the province of Cusco, to Miguel Condorcanqui Usquionsa Tupac Amaru, kuraka of three towns in the Tinta district, and María Rosa Noguera. On May 1, Túpac Amaru II was baptized by Santiago José Lopez in a church in Tungasuca. Prior to his father's death, Amaru II spent his childhood in the Vilcamayu Valley; he accompanied his father to community functions, such as the temple, the market, and processions. Tupac's parents died when he was twelve years old, and he was raised by an aunt and uncle. At age sixteen, he received a Jesuit education at the San Francisco de Borja School, founded to educate the sons of kurakas. The Jesuits "impressed upon him his social standing as future kuraka and someone of royal Inca blood." At age twenty-two, Túpac Amaru II married Micaela Bastidas. Shortly after his marriage, Amaru II succeeded his father as kuraka, giving him rights to land. As with his father, he was both the head of several Quechua communities and a regional merchant and muleteer, inheriting 350 mules from his father's estate. His regional trading gave him contacts in many other indigenous communities and access to information about economic conditions. His personal contacts and knowledge of the region were useful in the rebellion of 1780-81.
His status in the colonial Spanish racial hierarchy has been discussed by scholars, whether he was of "pure indigenous blood" or a mixed-race mestizo, although his mother most likely had partial Spanish ancestry. He was recognized as an elite Quechua from a kuraka family and was educated at a school in Cuzco for sons of indigenous leaders. He spoke Quechua and Spanish, and learned some Latin from the Jesuits. He was upwardly socially mobile, and in Cuzco he had connections with distinguished Spanish and Spanish American (creole) residents. "The upper classes in Lima saw him as a well-educated Indian," whatever European ancestry he might have had.
Between 1776 and 1780 Condorcanqui went into litigation with the Betancur family over the right of succession of the Marquisate of Oropesa and lost the case. In 1760, he married Micaela Bastidas Puyucahua of Afro-Peruvian and indigenous descent. Tupac Amaru II inherited the caciqueship, or hereditary chiefdom of Tungasuca and
Pampamarca from his older brother, governing on behalf of the Spanish governor.