Increasingly extreme weather events in high malaria burden areas threaten progress to disease control targets. Yet, data on the impact of these events on control programs remain rare. Using unique data from Madagascar, we estimate high rates of infection in the wake of two major tropical cyclones. Evidence that infection rebounds rapidly during gaps in interventions indicates maintaining continuity of coverage is crucial to limiting burden. Relative to other interventions, recently available malaria vaccines have a longer duration of protection, with the potential to address interruptions in prevention deployment. Evaluating this use case, we quantify the reduction in symptomatic infections expected for a range of vaccination scenarios. We find long-lasting interventions such as vaccination are a key mitigation measure against climatic disruptions to disease control.