The relationship between complex emergencies, health systems, and public health is a complex interaction in which pre-existing weak health systems result in poor public health outcomes for affected population while on the other hand complex emergencies negatively impact the health system of affected areas and create further health inequality for affected populations. It is therefore important to systematically manage the public health consequences of complex emergencies. Public health management of complex emergencies include preparedness, response, and recovery interventions which are underpinned by the principles of human rights, the right to health, equity which ensures no one is left behind, community participation, and sustainability. Moving forward, it is critical to regularly build the capacity of humanitarian stakeholders and partners on how to effectively manage the public health consequences of complex emergencies. This chapter summarizes the key principles and processes involved in the planning, implementing, coordinating, supervising, monitoring, and evaluating of public health response to complex emergencies.