The following is a list of khagans of the Northern Yuan Dynasty (1368–1388) and the Period of small khans (Döchin Dörben, 1388–1635) based in Northern China and the Mongolian Plateau.
Three Eastern Tumens Khalkha Chahar Uriankhai Three Western Tumens Ordos Tumed Yunshebu Tümen Choros Torghut Khoid Dörbet Oirat Yingchang Karakorum Hohhot Khagan Khan Khatun Taishi Jinong Khong Tayiji Noyan Tarkhan Councellor Wang Ukhaantu Khan Toghun-Temur (1368–1370) Biligtü Khan Ayushiridara (1370–1378) Uskhal Khan Tögüs Temür (1378–1388) Jorightu Khan Yesüder (1388–1391) Engke Khan (1391–1394) Elbeg Nigülesügchi Khan (1394–1399) Gün Temür Khan (1399–1402) Örüg Temür Khan Gulichi (1402–1408) Öljei Temür Khan Bunyashiri (1403–1412) Delbeg Khan (1411–1415) Oyiradai Khan (1415–1425) Adai Khan (1425–1438) Tayisung Khan Toghtoa Bukha (1433–1452) Agbarjin (1453) Esen Taishi (1453–1454) Markörgis Khan (Ükegtü) (1454–1465) Molon Khan (1465–1466) Manduul Khan (1475–1479) Dayan Khan (1480–1516) Bars Bolud Jinong (deputy) Bodi Alagh Khan (1516–1547) Darayisung Gödeng Khan (1547–1557) Tümen Jasaghtu Khan (1557–1592) Buyan Sechen Khan (1592–1604) Ligdan Khan (1604–1634) Ejei Khan (1634–1635) Altan Khan (1521–1582) Sengge Düüreng Khan (1583–1585) Namudai Sechen Khan (1586–1607) Boshugtu Khung Taiji (1608–1636) Barsu-Bolod (d. 1521) Mergen Jinong (d. 1542) Noyandara Jinong (1543–1572) Buyan Baatur Taiji (1573–1576) Boshugtu Jinong (1577–1624) Erinchen Jinong (1624–1636) Abtai Sain Khan (1567–1588) Eriyekhei Mergen Khan (1589–?)
Gombodorji Khan (d. 1655) Chakhun Dorji Khan (1654–1698) Laikhur Khan Subandai Khan Norbu Bisireltü Khan (d. 1661) Chambun Khan (1670?–) Zenggün Shara (d. 1687) Soloi Maqasamadi Sechen Khan (1577–1652) Baba Sechen Khan (1653–?)
Sechen Khan (d. 1686) Ubasi Khong Tayiji (c.1609–1623) Badma Erdeni Khong Tayiji (1623–1652) Erinchin Lobsang Tayiji (1652–1667)