The coronavirus disease 2019 (COVID-19) pandemic posed several challenges to the Brazilian health system, among them the general context of ambiguity and uncertainty and the conflicting positioning of the government in power concerning scientific advice resources. Different aspects can be analyzed to explore the dynamics of strengthening and resilience of the system. This paper focuses on its analytical capacity, examining how it was developed and recently challenged. The investigation employed survey data, analysis of official documents and newspaper articles, and in-depth interviews with specialists and federal bureaucrats. The research shows the magnitude and relevance of that dimension of policy capacity in the federal health system and how it was crucial to the resilience of the system in defining the directions of the fight against COVID-19 in Brazil, although scientific-based recommendations were rejected by political leaders.