The City of Nacogdoches has a council/manager form of government, whereby the elected City Council sets policies for the operation of municipal government. The administrative responsibility of the city rests with the City Manager, who is appointed by the city council. The city council consists of five members: a mayor (elected at-large) and four council members.
The Nacogdoches County government is administered by a Commissioners' Court system. The five-member Court is comprised of the county judge and four commissioners. The commissioners are elected by precinct, and the county judge is elected at-large. The Court is responsible for setting the county's annual tax rate, approving the tax roll and supervising all expenditures of county money. The Court is also responsible for issuing bonds to finance capital improvements.