The Chagatai Khanate is a khanate that comprises the lands ruled by Chagatai Khan, second son of Genghis Khan, and his descendants and successors.

Initially a part of the Mongol Empire, it becomes a functionally separate khanate with the fragmentation of the Mongol Empire after 1259.

The Chagatai Khanate recognizes the nominal supremacy of the Yuan dynasty in 1304, but the khanate becomes split into two parts, the Western Chagatai Khanate and Moghulistan, in the mid-fourteenth century.At its height in the late thirteenth century, the Khanate extends from the Amu Darya south of the Aral Sea to the Altai Mountains in the border of modern-day Mongolia and China.

The khanate lasts in one form or another from 1220s until the late seventeenth century, although the western half of the khanate is lost to the Timur's empire by 1370.

The eastern half remains under Chagatai khans, who are, at times, allied or at war with Timur's successors, the Timurid dynasty.

Finally, in the seventeenth century, the remaining Chagatai domains fall under the theocratic regime of Afaq Khoja and his descendants, the Khojas, who rule Xinjiang under Dzungar and Manchu overlordships consecutively.