Khonsa's history is intricately tied to the broader narrative of the Tirap district and its indigenous inhabitants. For centuries, the region was governed by the chieftains (Angs) of the Nocte, Wancho, and Tutsa tribes. These fiercely independent communities maintained their unique socio-cultural systems, relying on headhunting in ancient times—a practice long since abandoned—and sustaining themselves through traditional agriculture and trade with the neighboring plains of Assam.
During the British colonial era, the area remained largely unadministered, falling under the loosely defined "unadministered tracts" of the North-East Frontier Tracts. Following India's independence, the region was integrated into the North-East Frontier Agency (NEFA). Tirap was formally carved out as a district, and Khonsa was established as its headquarters in 1965, shifting the administrative base from its earlier location in Margherita (Assam).
In recent decades, Khonsa has evolved from a secluded tribal settlement into a modern town. The region experienced periods of unrest due to insurgent activities spilling over from neighboring Nagaland and Myanmar, but recent years have seen increased stability, a renewed focus on infrastructure, and a celebration of indigenous identity through peace initiatives and cultural preservation.