Early in the 13th century, the leader of the Mongolian people Genghis Khan established a Mongol Khanate north of China.In 1247 the Mongol Prince Godan invited Pandit Gonggar Gyaincain, an eminent monk with the Sagya Sect, to a meeting in Liangzhou (modern Wuwei in Gansu Province). He offered the submission of Tibet to the Mongol Khanate and the acceptance of a defined local administrative system and in return the Sagya were given political power in Tibet. In 1271 the Mongolian conquerors took Yuan as the name of their dynasty. In 1279 following their defeat of the Song they completed their unification of all of China. The newly united Central Government continued control over Tibet, including it as an administrative unit directly governed by the Chinese Yuan Dynasty Central Government.

In 1260, when Kublai Khan (1215-1294) ascended the throne, he conferred the title State Tutor on Gonggar Gyaincain's nephew Pagba, Prince of the Dharma of the Sagya order. In 1264 Kublai Khan established the Zongzhi (General) Council in charge of Buddhist affairs with Pagba at its head. It was renamed Xuanzheng (Political) Council. Under it was the Pacification Commission Chief Military Command responsible for handling military and government affairs over a large part of what is now Tibet. Below this level were Wan Hu Fu (10,000 household office) and Qian Hu Fu (1,000 household office) in charge of civil administration. In 1265 Kublai Khan honored Pagba with the titles of Great Treasure Prince of Dharma and Imperial Tutor. Following Pagba's recommendations he appointed an official for the overall management of Tibetan affairs and heads for 13 Wan Hu Fu. In 1268, 1287 and 1334 the Yuan Central Government sent officials to check on the Tibetan population. Fifteen staging posts were set up linking communications between Tibet and the Yuan capital Dadu (present-day Beijing). In addition, the Ula conscript labor system was established and promoted in Tibet.