The COVID-19 pandemic-associated learning losses were unequal across school subjects and sociodemographic groups. This study posits that these losses are also heterogeneous based on pre-pandemic school effectiveness, that is, the value schools added above the expected students’ learning based on their socioeconomic background. Using national-scale standardized mathematics and reading test scores, we compared learning losses between 2013–2018 (pre-pandemic) and 2022 at the school level in Chile and examined how they varied according to an indicator of schools’ pre-pandemic effectiveness. Schools with high effectiveness underwent the highest pandemic-driven losses, especially in mathematics. These losses were more pronounced as schools reopened later and students’ post-pandemic attendance decreased. Educational policies should adjust to this heterogeneity. While high-vulnerability, high-effectiveness schools require support to mitigate the pandemic’s effects, low-effectiveness schools must enhance their capacity to foster student learning beyond these impacts.