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During the early stages of the COVID-19 pandemic, almost all countries implemented school closures to prevent disease transmission. However, prolonged closures can put children at risk of leaving school permanently, a decision that can reduce their long-term potential and income. This study investigated the extent to which the COVID-19 pandemic and associated school closures reduced school attendance in Malawi, a low-income African country. We used longitudinal data from a cohort of adolescents interviewed before (2017/18; at age 10–16) and after (2021; at age 13–20) the pandemic school closures. Of those students who had been attending school prior to school closures, we find that 86% returned when schools re-opened. Dropouts were more pronounced among older girls: over 30% of those aged 17–19 did not return to school. This resulted in further lowering the gender parity index to the greater disadvantage of girls. We also found that students already lagging behind in school were more likely to dropout. Thus, our data suggest that the COVID-19 pandemic has magnified gender inequalities in schooling, at least partially erasing recent progress towards inclusive education. Urgent investments are needed to find and re-enroll lost students now, and to create more resilient and adaptable educational systems before the next pandemic or other negative shock arrives.