Long, long, ago, Ngari was one of 12 minor states of the Tibetan region, called Yangtung in the historical records of the Han People. After gradual development, Yangtung established the Kingdom of Zhangzhung between the 4th and 5th centuries. In the prime of its rule, the Kingdom divided its territory into inner, middle and outer parts. Inner Zhangzhung was, roughly, the current Ngari Prefecture. Around the seventh century, the Sibya Tribe, in the Yarlung River valley of Shannan, Tibet, developed and gradually expanded its territory to establish the Tubo Kingdom, with Shannan at the center. After Songtsan Gambo rose to the throne, he conquered the Dagbo, Gongbo, Nyangbo, Supi and some other tribes, following the victory of his predecessors in conquering some bordering tribes. In 644, he conquered Zhangzhung by force and unified the Tubo Kingdom. 

The last king of Tubo, Lang Darma, was killed in intensified internal conflicts. After his death, his two concubines, under the support of imperial kinsmen and others, fought for the throne for their sons and split the imperial court into two. During the rule of Lang Darma's grandsons, the two imperial courts suffered attacks from the populace and slave uprisings. Bekotsang, son of O'sum, second son of Lang Darma, was killed by the head of the slave army at Nanroshang Castle (Gyangze today). His son Gyide Nyimagun ran away to Zhabyran of Yangtung (Zhada County today) and married Melhu, daughter of a local official of Yangtung. They gave birth to three sons. After his sons grew up, Gyide Nyimagun, using the image as a mark, made an enfeoffment of historical significance: the eldest son Ribagun occupied Moyu, which centered around Leh of current Kashmir, Ribagun later becoming the leader of Ladakh; the second elder son Zhaxi Deguan held Burang, an area centering around the current Burang County, Tibet, and became the local leader; and the youngest son Dezogun occupied Zhabyran, an area centering around the current Zhada County. 

Dezogun followed his father's suit and became the head of Guge. The areas they ruled were called Burang Kingdom, Guge Kingdom and Ladakh Kingdom. Burang was described as a place where clouds meet, Guge (Zhabyran, and now Zhada) a place where clouds curve, and Moyu (Ladakh - Rutog) a place where clouds stand the highest. Henceforth, the large and small Yangtung areas, which were under the jurisdiction of the former Tubo Kingdom, were renamed "Ngari" (it means the three parts of Ngari). In later days, the three parts were gradually annexed by the Guge Kingdom established by Dezogun. 

Together with Tibet, the Guge Kingdom came under the jurisdiction of the Yuan Dynasty (1206-1368) in the 13th century, subordinate to the Pacification Commissioners General Office in the Three Regions of U, Tsang and Ngari. The charges of specific affairs in the Ngari region were turned over to the Sagya local administration. The Ming and Qing dynasties (1368-1911) basically followed the system of the Yuan Dynasty in terms of governing Tibet. After the fifth Dalai Lama established the Gandain Phodrang regime, Ngari was gradually incorporated into Gaxag (a local government of Tibet) under the support of the Qing Administration. Later, Zong (equal to county) and Ngari Jikyab, governor of Ngari, were established in the region. Ngari Prefecture was established following the Democratic Reform in 1959.