The foundation of Nerungri was directly related to development of South Yakutia's natural riches. The first information about these lands was attained by the Russian pathfinders Vasily Poyarkov (1643) and Yerofey Habarov (1667). They went from Yakutsk to Amur and the Far East. From the beginning of the 19th century this area was actively investigated by expeditions organized by the Russian Academy of Sciences, Geographical Society and Ministry of Railways. Its industrial development started in 1891 — 1892. There were about 80 mines in the upper courses of Rivers Timpton, Sutam and their inflows back then. Up to 3,5 thousand gold prospectors seasonally lived there.

In the 1940s it was a place for location of a prospecting batch.

The start of building the northern branch of BAM (of the BAM line Tynda — Berkakit) and generating of the Southern Yakut territorial and production complex in 1975 opened a new page in the history of Nerungri. On November 5, 1975 it was transformed into a city.