PurposeGovernments faced formidable challenges in coordinating public health responses to the COVID-19 pandemic. This study aims to enhance the understanding of effective organizational leadership during crises by investigating the factors influencing the turnover of health leaders during the COVID-19 pandemic in Brazil.Design/methodology/approachUsing primary data encompassing all appointments and dismissals of federal and state health secretaries, this paper conducted a quantitative analysis of the relational and reputational factors that contributed to leader turnover during the COVID-19 pandemic. This paper also examined whether leaders’ management and public health experience increase the duration of tenure.FindingsStates encountered significant challenges in retaining experienced and effective leadership during the health emergency, primarily due to political conflicts in policymaking and, to a lesser extent, allegations of corruption. Furthermore, leaders with expertise in public health were found to be less likely to be removed from office. However, managerial experience did not prolong the tenure of state health secretaries during the emergency.Research limitations/implicationsSince most health leaders have public health and management experience, the contributions of each factor to the duration of a secretary’s tenure are difficult to separate and analyze separately.Practical implicationsThis study provides empirical insights into what factors drive health leader turnover during major health emergencies.Social implicationsDuring major health emergencies, health leaders often strongly disagree with elected officials on the response. This paper test how crisis leadership theories help explain state health leaders’ duration in one of the world’s largest public health systems during the COVID-19 pandemic. This paper find that policy disagreements contributed to significant turnover.Originality/valueTo the best of the authors’ knowledge, this paper is the first that are aware of that uses novel primary data on public health executive leader characteristics and turnover causes in the context of the COVID-19 pandemic. It provides empirical evidence contributing to the crisis leadership literature by examining health leader turnover in one of the world’s largest public health systems.