Emerging evidence suggests that rural children, particularly older girls in low-income countries, are at risk of being withdrawn from school when weather-related disasters occur. Identifying actions that mitigate the adverse effects of weather shocks on school enrolment, therefore, is critical for sustaining equitable human capital formation in the context of climate change. In this paper, we use four waves of household and community panel survey data, merged with long-term, spatially explicit rainfall data to investigate whether access to school feeding programmes (SFP) in Malawi supports primary school enrolment when weather shocks occur. We find that access to SFP increases enrolment of children in older age when households experience anomalously low rainfall conditions compared to those without a SFP. The positive impacts of SFP on enrolment for older children remain when we consider the role of SFPs in addressing historical shocks over longer periods. When disaggregated by gender, we find particularly relevant benefits of these programmes for girls in older age in rural areas. These findings suggest that SFPs are an important tool for helping to improve primary school completion rates, educational advancement, and human capital formation in the context of a rapidly changing climate.