The COVID-19 outbreak has created an uncertain scenario for educational systems, leading many countries to deploy unprecedented remote learning programmes. Chilean schools have not been the exception and have thus developed and put in place several actions to uphold effective pedagogical management (PM) and continuity of learning; however, as we emphasise in this paper, the Chilean educational system is highly segregated. PM encompasses actions and decisions aimed at safeguarding quality education by focusing on four domains: technological, curricular, methodological and assessment. This descriptive and exploratory quantitative study seeks to explore the challenges facing PM, as perceived by actors working in Chile's three different administrative and financial school governance systems in the framework of remote education during the COVID-19 pandemic. Our findings highlight the disparities among actors belonging to the three types of administrative and financial governance systems regarding the perceived challenges facing PM. Thus, publicly funded schools face greater challenges in practically all four PM domains as compared to private schools. The main differences among schools revolve around the technological and assessment domains. While the technological domain is more of a concern for public schools, the assessment domain presents more challenges for private schools. Beyond the schools´ administrative and financial governance system, an important finding was the scant importance attached to the curriculum as a challenging issue as well as an excessive focus on the methodological domain, indicative of a prevailing logic of efficiency as applied to the learning process.