The outbreak of coronavirus disease 2019 (COVID-19) has exerted unprecedented pressure on healthcare systems throughout the world. This study was designed to develop a national health emergency management program based on risk assessment for COVID-19.

Mixed-methods research was used. Based on recommendations of the national epidemiology committee, 2 risk scenarios were used as basic scenarios for risk assessment. Two rounds of Focus Group Discussions (FGDs) were conducted between January and May 2020 with 30 representatives of the health system. The data were collected, analyzed, and integrated by the research team.

In the risk matrix, “contamination of environment and individuals” and “burnout of medical staff” occupied the red zone (intolerable risk). “Defects in screening and admissions,” “process disruption in medical care and rehabilitation,” “increased mental disorders,” “social dissatisfaction,” “the decline in healthcare services,” and “loss of medical staff” were identified as the orange zone (significant risk) of the matrix.

The avoidance of environmental and individual contamination and healthcare worker burnout are the priorities in Iran. Attention to intersectoral cooperation, the involvement of non-governmental organizations and private center capacities, integration of information health systems, and developing evidence-based protocols are other measures that can improve the health system’s capacity in the response COVID-19.