Climate disruptions are increasingly affecting retention of girls in secondary schools in rural Malawi, a country highly vulnerable to extreme weather events. However, empirical evidence on how adaptive planning and feedback mechanisms by Non-Governmental Organizations (NGOs) support girls’ retention during climate shocks remains limited. This study employed a qualitative multi-case study approach, guided by three objectives: (1) to identify the main climate-related disruptions affecting female students; (2) to describe how NGOs implement adaptive planning and feedback mechanisms in supporting female student retention; and (3) to explore stakeholder perceptions of how these mechanisms support girls’ retention. Four Community Day Secondary Schools (CDSSs) in rural Phalombe District were purposively selected. Data were collected through semi-structured interviews (n=54) and focus group discussions (n=100) targeting female students, teachers, Parent-Teacher Associations (PTA) members, mother groups, NGO staff, and community leaders. Thematic analysis was conducted using NVivo 15. Findings show that repeated flooding and cyclones disrupted learning through infrastructure damage, prolonged school closure, displacement, and food insecurity. These disruptions increased gendered vulnerabilities including increased domestic burdens, early marriage, transactional sex, sanitation challenges and safety risks for girls. Adaptive planning was predominantly reactive and non-gender-sensitive, with no school having a disaster preparedness plan. Feedback systems failed to meaningfully engage girls in decision-making processes, as parents, teachers, and community leaders dominated consultations. As a result, the current mechanisms inadequately supported retention, with selective NGO support exacerbating inequalities. Therefore, the study recommends that NGOs and donors strengthen inclusive engagement, adopt proactive gender-sensitive adaptive planning, and establish formal coordination mechanisms among schools, district education offices and NGOs to sustain girls' education during escalating climate disruptions.