Zunheboto is administered locally by the Zunheboto Town Council (ZTC), which oversees municipal functions such as sanitation, local infrastructure, and urban planning. As the district headquarters, it is also the seat of the Deputy Commissioner (DC), who represents the state government and is responsible for law and order, revenue collection, and the implementation of development schemes.
The town falls under the Zunheboto Assembly constituency, sending a representative to the Nagaland Legislative Assembly. Traditional governance also plays a role in community life; customary laws and tribal councils often mediate local disputes and organize community efforts, working in tandem with formal government structures.