[1]: 10  After the death of his mother in 1539 and of his father in 1544, both at the hands of Spanish conquerors, he became the ruler of the Neo-Inca State in Vilcabamba.

Sayri Tupac's father Manco, the last ruling Inca emperor, had attempted to reach an accommodation with the Spanish conquistadors.

Viceroy Pedro de la Gasca offered to provide Sayri Túpac with lands and houses in Cuzco if he would emerge from the isolated Vilcabamba.

In return he received a full pardon, the title of Prince of Yucay, and great estates with rich revenues.

Significantly, he left behind the Mascaipacha, a crown with red fringe, which was the symbol of his authority as Sapa Inca over the Incan Empire.

In Cuzco, he married his sister Cusi Huarcay after receiving a special dispensation from Pope Julius III.