The Dzungar Khanate (Mongolian: ᠵᠡᠭᠦᠨᠭᠠᠷ ᠣᠯᠣᠰ Зүүнгар Улс), also known as the Zunghar Khanate or Junggar Khanate, was a nomadic khanate of Oirat Mongol origin. At its greatest extent, it covered an area from southern Siberia in the north to present-day Kyrgyzstan in the south, and from present-day west of Mongolia and the Great Wall of China in the east to present-day Kazakhstan in the west. The core of the Dzungar Khanate is today part of northern Xinjiang, also called Dzungaria.

About 1620 the western Mongols, known as the Oirats, united in the Junggar Basin in Dzungaria. In 1678, Galdan received from the Dalai Lama the title of Boshogtu Khan, making the Dzungars the leading tribe within the Oirats. The Dzungar rulers used the title of Khong Tayiji, which translates into English as "crown prince". Between 1680 and 1688, the Dzungars conquered the Tarim Basin, which is now southern Xinjiang, and defeated the Khalkha Mongols to the east. In 1696, Galdan was defeated by the Qing dynasty and lost Outer Mongolia. In 1717, the Dzungars conquered Tibet, but were driven out in 1720 by the Qing. From 1755 to 1758, Qing China took advantage of a Dzungar civil war to conquer Dzungaria and killed 70–80% of the Dzungar population. The destruction of the Dzungars led to the Qing conquest of Mongolia, Tibet, and the creation of Xinjiang as a political administrative unit.

"Dzungar" is a compound of the Mongolian word jegün (züün), meaning "left" or "east" and γar meaning "hand" or "wing". The region of Dzungaria derives its name from this confederation. Although the Dzungars were located west of the Khalkas, the derivation of their name has been attributed to the fact that they represented the left wing of the Oirats. In the early 17th century, the head of the Oirat confederation was the leader of the Khoshut, Gushi Khan. When Gushi Khan decided to invade Tibet to replace the local Tsangpa khan in favor of rule by the Gelug, the Oirat army was organized into left and right wing. The right wing consisting of Khoshuts and Torguts remained in Tibet while the Choros and Khoid of the Left wing retreated north into the Tarim basin, since then the powerful empire of the Choros became known as the Left Wing, i.e. Zuungar.

The region was separately described in contemporary European sources as the Kingdom of the Eleuths, from an infelicitous transcription of the name "Oirats" by French missionaries. This was sometimes vaguely extended to cover wide areas of Central Asia, including Afghanistan.

The Oirats were originally from the area of Tuva during the early 13th century. Their leader, Quduqa Bäki, submitted to Genghis Khan in 1208 and his house intermarried with all four branches of the Genghisid line. During the Toluid Civil War, the Four Oirat (Choros, Torghut, Dörbet, and Khoid) sided with Ariq Böke and therefore never accepted Kublaid rule. After the Yuan dynasty's collapse, the Oirats supported the Ariq Bökid Jorightu Khan Yesüder in seizing the Northern Yuan throne. The Oirats held sway over the Northern Yuan khans until the death of Esen Taishi in 1455, after which they migrated west due to Khalkha Mongol aggression. In 1486, the Oirats became embroiled in a succession dispute which gave Dayan Khan the opportunity to attack them. In the latter half of the 16th century, the Oirats lost more territory to the Tumed.

In 1620, the leaders of the Choros and Torghut Oirats, Khara Khula and Mergen Temene, attacked Ubashi Khong Tayiji, the first Altan Khan of the Khalkha. They were defeated and Khara Khula lost his wife and children to the enemy. An all out war between Ubashi Khong Tayiji and the Oirats lasted until 1623 when Ubashi Khong Tayiji was killed. In 1625, a conflict erupted between the Khoshut chief Chöükür and his uterine brother Baibaghas over inheritance issues. Baibaghas was killed in the fight. However, his younger brothers Güshi Khan and Köndölön Ubashi took up the fight and pursued Chöükür from the Ishim River to the Tobol River, attacking and killing his tribal followers in 1630. The infighting among the Oirats caused the Torghut chief Kho Orluk to migrate westwards until they came into conflict with the Nogai Horde, which they destroyed. The Torghuts founded the Kalmyk Khanate but still stayed in contact with the Oirats in the east. Every time a great assembly was called, they sent representatives to attend.

In 1632, the Gelug Yellow Hat sect in Qinghai was being repressed by the Khalkha Choghtu Khong Tayiji, so they invited Güshi Khan to come and deal with him. In 1636, Güshi led 10,000 Oirats in an invasion of Qinghai which resulted in the defeat of a 30,000 strong enemy army and the death of Choghtu. He then entered Central Tibet, where he received from the 5th Dalai Lama the title of Bstan-'dzin Choskyi Rgyal-po (the Dharma King Who Upholds the Religion). He then claimed the title of Khan, the first non-Genghisid Mongol to do so, and summoned the Oirats to completely conquer Tibet, creating the Khoshut Khanate. Among those involved was Khara Khula's son, Erdeni Batur, who was granted the title of Khong Tayiji, married the khan's daughter Amin Dara, and sent back to establish the Dzungar Khanate on the upper Emil River south of the Tarbagatai Mountains. Batur returned to Dzungaria with the title Erdeni (given by the Dalai Lama) and much booty. During his reign he made three expeditions against the Kazakhs. The conflicts by the Dzungars are remembered in a Kazakh ballad Elim-ai. The Dzungars also went to war against the Kyrgyz, Tajiks, and Uzbeks when they invaded deep into Central Asia to Yasi (Turkestan) and Tashkent in 1643.

In 1653, Sengge succeeded his father Batur, but he faced dissent from his half brothers. With the support of Ochirtu Khan of the Khoshut, this strife ended with Sengge's victory in 1661. In 1667 he captured Erinchin Lobsang Tayiji, the third and last Altan Khan. However, he himself was assassinated by his half-brothers Chechen Tayiji and Zotov in a coup in 1670.