Background: Malaria is a serious disease and still remains a public health problem in many parts of Nigeria. Objectives: The aim of this study was to describe malaria transmission trends and analyzed the impact of climatic factors on malaria transmission in the highlands of Plateau State, Central Nigeria. Methods: The study was a retrospective survey which used archival data of climate parameters and medical case records on malaria. Rainfall, relative humidity, and temperature data were obtained from the nearest weather stations to the study locations from 1980 to 2015. Data on reported malaria cases were collected from general hospitals in the selected local government areas (LGAs) from 2003 to 2015. Generalized Additive Models were used to model trends in malaria incidences over time, and it is lagged association with climatic factors. Results: The results show a significant cyclical trend in malaria incidence in all the study areas (P < 0.001). The association between monthly malaria cases and mean monthly temperature, rainfall, and relative humidity show significant association at different time lags and locations. Conclusion: Our findings suggest that climatic factors are among the major determinants of malaria transmission in the highlands of Plateau state except in Jos-North LGA where the low model deviance explained (35.4%) could mean that there are other important factors driving malaria transmission in the area other than climatic factors.