The Mayor of Zamboanga City and is the head of the executive branch of the Zamboanga City's government. The mayor holds office at Zamboanga City Hall. Like all local government heads in the Philippines, the mayor is elected via popular vote, and may not be elected for a fourth consecutive term. In case of death, resignation or incapacity, the vice mayor becomes the mayor.

The Government of Zamboanga City, also known as the Zamboanga City Government is the local government unit in-charge of the City of Zamboanga. It is a mayor-council form of government supervised directly by the President of the Philippines and the Secretary of the Interior and Local Government.