Although infant mortality has decreased in the world in recent years, countries in Sub-Saharan Africa are still struggling with high prevalence of infant deaths. Using Demographic and Health Survey (DHS) and high resolution rainfall and temperature estimates, we investigate how weather conditions could affect an infant’s survival in Mali. Applying survival analysis, we find that high rainfall amount during the growing season and heat stress during the dry season negatively affect an infant’s survival in rural areas, but not in urban areas. Furthermore, there are significant prenatal weather effects on infants, suggesting that pregnant mothers’ exposure to heat, disease or malnutrition could negatively affect child health. The findings suggest that healthcare in rural communities should take a priority in public health policy debates in mitigating infant deaths in the future.