The Xiongnu Empire (209 BC – AD 93) governed the territory of the modern Altai Republic. The area was part of the First Turkic Khaganate, the Uyghur Empire, and the Yeniseian Kyrgyzs. It was during this time that the local population became fully Turkicized culturally and linguistically.[11]

The southern part of the Altai Republic came under the Naiman Khanate. The territory of the modern Altai Republic has been ruled by the Mongolic Xianbei state (93–234), Rouran Khaganate (330–555), Mongol Empire (1206–1368), Golden Horde (1240–1502), Zunghar Khanate (1634–1758) and Qing Empire (1757–1864).

The Qing period is a semi-autonomous period with the supervision of two Altan Nuur Uriankhai Governor Banners and part of the seven Altai Uriankhai banners. During the Qing administration, the General of Siberia Fedor Ivanovich Soimonov launched a non-military expedition into the Altan Nuur region in 1760 and began fort building. This was subsequently removed by Heseri Jalafungga of the Qing. Since the 1820s, the routine border check was less frequent and the Chuy drainage basin has been occupied by Russians.

The entire Altan Nuur Uriankhai region was annexed into the Russian Empire in 1864–1867 by the Treaty of Tarbagatai. During the Russian Civil War, the Confederated Republic of Altai (Karakorum-Altai Region) was established in 1918, and declared as the first step to rebuilding Genghis Khan's Mongol Empire.[12] But it never became a competing force in the Russian Civil War, and stayed neutral from 1918 until January 1920, when it was annexed back into Russia. A second Altai Republic was formed in 1921 and lasted until 1922 when they were annexed by the Bolsheviks.[12]

On June 1, 1922, the Altaians regained autonomy with the creation of the Oyrot Autonomous Oblast (Ойро́тская автоно́мная о́бласть), part of Altai Krai. The original name for this region was Bazla. On January 7, 1948, it was renamed Gorno-Altai Autonomous Oblast (Го́рно-Алта́йская автоно́мная о́бласть). In 1991 it was reorganized into the Gorno-Altai Autonomous Soviet Socialist Republic (ASSR). In 1992 it was renamed as the Altai Republic.