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

Initially it is a part of the Mongol Empire, but it later becomes fully independent when the Yuan Dynasty falls in the late 14th century.

The Chagatai Khans themselves recognize the sovereignty of the Mongolian Khagans between 1206 and 1270 and 1304 and 1368.

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 17th century, although the western half of the khanate is lost to Tamerlane in the 1360s.

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

Finally, in the 17th century, the remaining Chagatai domains fall under the theocratic regime of Apaq Khoja and his descendants, the Khojijans, who rule Xinjiang under Dzungar and Manchu overlordships consecutively.