Abstract: Malaria is one of life’s threatening disease that contributed significantly to morbidity and mortality in Nigeria. The variability effects of meteorological factors between the Northern and Southern region of Nigeria on malaria transmission remain unclear and not well researched. This research was aimed at comparing the non-linear effects of seasonal, trend and meteorological variables on monthly malaria cases in Kano and Lagos State of Nigeria. The monthly malaria cases for age group above 5-year for Kano and Lagos State were obtained from DHIS for the period of January, 2016 to December, 2022. Also, the predictors/meteorological variables (Rainfall, Relative Humidity, Minimum Temperature and Maximum Temperature) were obtained from Nigeria Meteorological Agent. Generalized Additive Model was fitted using Negative Binomial to apply smooth function to estimate and compare the effects of the selected predictors on the malaria transmission in Kano and Lagos States. Rainfall and Maximum temperature were found not significant in explaining the effect of malaria transmission. Malaria transmission was found to be seasonal and varying in Kano State with highest transmission between September and October while the seasonal effect was reduced to linear in Lagos State. The long term trend had a significant increasing effect on malaria transmission in Kano Sate compared to non-significant effect in Lagos State. The effect of Relative Humidity was reduced to linear and increasing in the both State. Paying attention to the variability in the influence of season, trend and meteorological variables on malaria transmission will enhance respective State Government to develop an early warning and awareness that will help in controlling the malaria outbreak in their State.