Nagqu has a long history. Since the 1950s geologists and archaeologists have discovered numerous stone artifacts in the Northern Tibet Plateau, which in their shape and method of production reflect the nomadic culture of the area, and date to the mid and late palaeolithic era some 10,000-50,000 years ago. According to historical records, this part of the world was controlled by the Zhangzhong polity. In Chinese sources it is referred to as Yangtong, while in Tibetan historical records it is called Chodai which means "herding tribe." Residents of Chodai are called "Changpa" meaning northerners, or "Changri" meaning northern tribe. At the peak of the Zhangzhong polity, the area was divided into three sections: interior, central and exterior Zhangzhong. Today's Nagqu Prefecture covers the former central and exterior Zhangzhong. 

The middle of central Zhangzhong or "Tangra Qoingzong" lies in the Tangra Yumco Lake area in southwestern Nagqu Prefecture. Zhangzhong diminished in size towards the west when the polity was in decline. Around the 7th century, the eastern area came under the domination of the Supi tribe. When the Tubo tribe later unified the whole of Tibet and founded the Tubo Kingdom, northern Tibet was incorporated into its sphere of influence. During the reign of the Tubo king Songtsan Gambo, Tubo was composed of four "tai" and 61 "domdai" equivalent to 1,000-household offices. "Sumboru" was established in the area formerly under the Supi tribe, and exercised jurisdiction over 11 "domdai.." As the base for the Tubo as they expanded into the Western Regions and the Hehuang and Jiangming areas, Sumboru was of great importance. According to historical records, "half of the military food grain and horses came from the area." 

After 1279, Nagqu became one of the Four Northern Tribes, which also incorporated Yangbajain, Bamcang (today's Tangra Yumco Lake and Ngangzi Co Lake area) and Langru (present-day Bangoin). In 1269, Kublai Khan sent his Yuan officials to set up post stations on the major postal routes from Qinghai to Sasgyia, which included seven in the Lhasa area. The postal routes extended through present-day Nagqu's Baqen, Sog, Biru, Nagqu and Damzung. Mongolian troops were stationed in northern Tibet, and the Mongolian forces known as the 39 Tribal Hor were gradually established in the area. In 1725, the Qing (1644-1911) government appointed an official to Qinghai to administer local affairs. The 12th "king of Hor" Chigyai Gyiqen was also put in charge of the 39-Tribal Area under the leadership of the Ethnic Affairs Office of the Qing Commission for Mongolian and Tibetan Affairs. In 1728, the Qing government established the High Commissioner Office in Lhasa, and three years later made moves to determine the border between Qinghai and Tibet. 

In 1731, the various tribes in the southern and northern Tanggula Mountains came under the control of the Qing High Commissioner and the Minister for Qinghai, and the 39-Tribal Area came under the control of the Qing High Commissioner. In the same year, a population census was conducted among the various tribes, which were required to pay corvee to the Qing Dynasty High Commissioners Office. By 1907, the 33rd year of the reign of the Qing emperor Guangxu, eight generations of "Hor kings" had been granted official positions by the Qing government. In 1751, when the Qing court sent troops to frustrate the plot engineered by Gyurmed Namugyal, the government implemented a 13-article Ordinance for the More Effective Governing of Tibet, which included a major reform of the administrative system. 

Given the geographical location of Nagqu and its strategic importance for the suppression of riots in Tibet, the Qing government established Kamxian County which followed the temporal and religious administration. Part of Nagqu was controlled by the Panchen Erdeni. During the Revolution of 1911, the Qing government was toppled. This made it possible for the Gaxag government to take over area directly under the Qing High Commissioners and the 39-Tribal area. When the 9th Panchen Erdeni was forced to China's hinterland, the Gaxag government forcibly seized control of area formerly controlled by the Panchen Erdeni. For the first time following the fall of Tubo Kingdom, northern Tibet came under the Gaxag government. In order to tighten control of Dermo and the 39-Tribal area, the Gaxag government installed horkyi or the Hor chief manager. This put an end to the 500-year history of 21 generations of Hor kings. There were nine generations of Horkyi in history. In 1942, the Gaxag government rescinded the post of Horkyi, and installed Jamqoi Kyicho or the Nagqu Administration in northern Tibet for rule over the pastoral area in northern Tibet and the 14 counties north of Lhasa. By 1959, there were five generations of Nagqu chief managers. Each was of fourth ranking official position, and edch position was shared by one monk and one lay official. 

In October 1950, Qamdo and eastern Nagqu won liberation. The Qamdo people's Liberation Committee was established in March of the following year. Counties formerly under Jamqoi Kyicho, including Nyirong, Sog, Baqen, Biru, Lhari, Chido, Sezha and Dengqen, came under the control of the First office of the Liberation Committee stationed in Dengqen. After the signing of the 17-Article Agreement for the Peaceful Liberation of Tibet in 1951, some 2,000 members of the main force of the PLA 18th Army escorted the 10th Panchen Erdeni back to Tibet via northern Tibet. Nagqu, which was formerly under the control of the Panchen Erdeni was naturally returned to him. January 1953 saw the founding of the CPC Tibet Work Committee and the Hehei Branch Committee. On October, 9,1956, the Preparatory Committee for the Founding of the Tibet Autonomous Region established the heihe kyicho Office. 

After the Democratic Reform of 1959, the Preparatory Committee for the Founding of the Tibet Autonomous Region readjusted the administrative division of northern Tibet and the Hehei Kyicho controlled nine counties. In October 1959, the Preparatory Committee decided to disband the Kyicho Offices in various localities and establish an Administrative Office. Four months later, the Heihe Commissioner's Office was set up, and in 1965 this became the Nagqu Administrative Office. Nyima County was established with the approval of the State Council in 1985. From this time onwards, the Nagqu area has consisted of 10 counties and one district.