This dataset provides monthly malaria incidence rates and associated climatic variables (temperature, rainfall, and relative humidity) for Jigawa, Kaduna, Kano, Katsina, Kebbi, Sokoto, and Zamfara States, Nigeria, from January 2015 to December 2024. The data were used to examine malaria seasonality, climate-malaria lead-lag relationships, and cross-state transmission synchrony using wavelet-based analyses.