The City of Hughson operates under a Council-Manager form of Government. The voters elect the City Council and the Council appoints the City Manager. The City Manager appoints all subordinate employees of the City of Hughson with the exception of the Treasurer, the City Attorney and the various Boards and Commissions.

The City Manager serves as the Chief Executive Officer of the City and directs the activities and operations of all departments, assists the City Council in the conduct of City business and provides administrative oversight to the operation and policy function of the City Government. The City Manager also serves as a Board Member to the Oversight Board of the Successor Agency to the Redevelopment Agency for the City of Hughson.