The civic administration of the town is managed by the Mokokchung Municipal Council (MMC), which is responsible for public sanitation, urban planning, local road maintenance, and water supply coordination. The municipality is divided into several wards, each electing representatives to the council.
At the district level, the administration is headed by a Deputy Commissioner (DC), a civil servant appointed by the state government, who oversees law and order, land revenue, and developmental programs. Mokokchung district is a crucial political constituency in Nagaland, sending ten elected representatives to the Nagaland Legislative Assembly, ensuring the city and its surrounding areas have significant political influence within the state.