In the late 12th century, the Mongol Genghis Khan conquered much of north China. He even captured the territory of the Western Xia Regime.

When he died, his third son came to power. Forces in Amdo, Kkam and u-Tsang pledged allegiance to him. In 1240, Prince Godan sent General Dorda Napo into Tibet via Amdo and the Kham area. Those who supported them were given protection, and those who resisted were suppressed. In northern Tibet, they killed 500 monks from the Razheng Monastery. Prince Godan investigated the various religious sects in Tibet and suggested Godan meet Sagya Pandit, who was believed to have a good command of the Buddhist doctrines.

Sagya Pandit was then aged 63. He went together with two of his nephws-10-year-old Pagba and 6-year-old Chana Dorje-to meet Godan in Liangzhou, and the latter then wrote an open letter to others in Tibet, calling on them to pedge allegiance to the Yuan Dynasty.

In 1260, when Khublai Khan came to power and the Yuan Dynasty was formally established, Pagba was honored as State Tutor and Imperial Tutor to head the board in charge of Mongolian and Tibetan Buddhist affairs; and Chana Dorje was honored with the title of Prince Bailan. Thus, the Sagyapa Regime was founded.

The Yuan strengthened rule over Tibet by giving official posts to heads of the Sagyapa Regime, conducting a census in Tibet, and setting up military posts. This, in turn, helped the Sagyapa Regime to last for about 100 years. In 1358 Jamqoi Gyaincain, head of the Pagmo Zhuba 10,000-House, captured Sagya and replaced the Sagyapa with the Pagmo Zhuba Regime.