Objectives: Since 9/11, Incident Command System (ICS) and Emergency Operations Center (EOC) are relatively new concepts to public health, which typically operates using less hierarchical and more collaborative approaches to organizing staff. This paper describes the 2009 H1N1 influenza outbreak in San Diego County to explore the use of ICS and EOC in public health emergency response. Methods: This study was conducted using critical case study methodology consisting of document review and 18 key-informant interviews with individuals who played key roles in planning and response. Thematic analysis was used to analyze data. Results: Several broad elements emerged as key to ensuring effective and efficient public health response: 1) developing a plan for emergency response; 2) establishing the framework for an ICS; 3) creating the infrastructure to support response; 4) supporting a workforce trained on emergency response roles, responsibilities, and equipment; and 5) conducting regular preparedness exercises. Conclusions: This research demonstrates the value of investments made and that effective emergency preparedness requires sustained efforts to maintain personnel and material resources. By having the infrastructure and experience based on ICS and EOC, the public health system had the capability to surge-up: to expand its day-to-day operation in a systematic and prolonged manner. None of these critical actions are possible without sustained funding for the public health infrastructure. Ultimately, this case study illustrates the importance of public health as a key leader in emergency response.