Despite notable investments in education, persistent gender gaps in educational attainment remain in developing countries. One potential explanation is that climate induced disease events can limit the effectiveness of these investments in closing the gap. We investigate this hypothesis by examining the effects of sudden exposure to the 1986 meningitis epidemic in Niger on the gender gap in education. We document a significant reduction in years of education for school-aged girls relative to boys following the epidemic. We explore several channels underlying the results and find evidence highlighting income effects of epidemics on households and increased early marriage of girls.