Naharlagun's history is inextricably linked to the establishment of Itanagar as the capital of Arunachal Pradesh in 1974. Prior to its modern urbanization, the area was primarily inhabited by the indigenous Nyishi tribe, who practiced traditional farming and lived in harmony with the region's dense forests and rivers.
When the decision was made to build a new capital at Itanagar, the lower-elevation area of Naharlagun served as the natural staging ground and entry point for construction materials, government officials, and laborers. Over the decades, it evolved from a temporary transit camp into a permanent, thriving settlement. It absorbed a significant portion of the commercial and residential spillover from Itanagar.
A watershed moment in the city's modern history occurred in 2014, when the Naharlagun Railway Station was inaugurated by the Prime Minister of India. This brought the first broad-gauge railway line to the state, ending decades of total reliance on road transport and fundamentally altering the economic trajectory of the city. In 2018, the inauguration of the Tomo Riba Institute of Health & Medical Sciences (TRIHMS) further cemented Naharlagun's importance as a regional center for healthcare and education.