Transposing rule of law principles from the national to the international level, in particular to international organizations, still raises questions and can be problematic. However, rule of law considerations play an important role when international organizations exercise a substantial amount of public authority and may directly affect states as well as individuals. The World Health Organization (WHO), unlike other international organizations, has a constitutional mandate to prevent and respond to international acute emergencies in the form of disease outbreaks and pandemics. Its main normative tool is the 2005 International Health Regulations (IHR), that represent a breakthrough from past instruments but also raise questions and challenges that can be effectively analyzed from a rule of law perspective. This approach applies in particular to ambiguities in important parts of the IHR affecting their relevance and effectiveness; lack of clarity for processes leading to sensitive executive decisions; the absence of compliance assessment mechanisms resulting in lack of accountability for states parties; and an inadequate inclusion of human rights guarantees. The analysis is extended beyond WHO’s functions, to the impact of COVID-19 on the organization’s governance as well as its internal management.