Khonsa operates under a district administration model, serving as the headquarters for the Tirap district. The town and district are administered by a Deputy Commissioner (DC), an Indian Administrative Service (IAS) officer appointed by the state government, who oversees law and order, development, and revenue collection.
Local governance within the town limits is managed by an urban local body or town committee that handles sanitation, local roads, and public services. Politically, Khonsa is represented in the Arunachal Pradesh Legislative Assembly through two constituencies: Khonsa East and Khonsa West. At the national level, the town falls under the Arunachal East Lok Sabha constituency. The traditional village council systems, led by the village chief (Ang), still hold immense social and customary authority in the surrounding villages.
