The City of San Juan Capistrano operates within the Council-Manager system of local government that combines the strong political leadership of elected officials in the form of a council, with the strong managerial experience of an appointed local government city manager. The city manager is appointed by council to carry out policy and ensure that the entire community is being served.
The City Manager's Office provides oversight of all City personnel and line departments and ensures that the City Council priorities are understood and implemented in partnership with area stakeholders and other government entities. Within the City Manager's Office are several divisions including Human Resources and Risk Management, Public Safety and Emergency Management, Open Space and Real Estate Management, Information Technology, and Special Projects.