Public health emergency management systems encountered difficulties in developing countries, especially in Pakistan. The COVID-19 pandemic was extremely challenging for different agencies/departments in Pakistan. Health emergency management depends on a well-established public health emergency operations center that could generate a coordinated response to emergencies. We conducted an assessment of public health emergency response coordination implemented during the COVID-19 at strategic level. This was mix-method qualitative study. Primary data was collected by using a structured questionnaire, and secondary data was collected by desk review. The agencies engaged in pandemic response at the national level in Pakistan were included in the assessment. The overall score of the emergency response coordination system during COVID-19 was 49% for all agencies. We found that agencies faced challenges in leadership, legislation, and financing issues during the pandemic response (44%). None of the agencies had a fully developed framework for joint planning and response system for health emergencies. Roles and responsibilities attached to designated agencies in response were relatively clear (55%) for most of the agencies. Effective public health emergency response is based on multi-departmental coordination, resource mobilization, and clear roles for each agency. Pakistan must proactively address these challenges for pandemic response in future.