Background and objectives: Malaria is among the most important parasitic diseases, and is one of the endemic diseases in Iran. This disease is often known as a disease related to climate changes. Due to the health and economic burden of malaria and the location of Kerman province in an area with high incidence of malaria, the present study aimed to evaluate the effects of climatic factors on the incidence of this disease. Material and methods: Data on the incidence of malaria in Kerman province was inquired from Kerman and Jiroft Medical Universities and climatic variables were inquired from the meteorological organization of Kerman. The data was analyzed monthly from 2000 to 2012. Variations in incidence of malaria with climatic factors were assessed with negative binomial regression model in STATA11software. In order to determine the delayed effects of meteorological variables on malaria incidence, cross-correlation analysis was done with Minitab16. Results: The most effective meteorological factor on the incidence of malaria was temperature. As the mean, maximum, and minimum of monthly temperature increased, the incidence rate raised significantly. The multivariate negative binomial regression model indicates that a 1 °C increase in maximum temperature in a given month was related to a 15% and 19% increase on malaria incidence on the same and subsequent month, respectively (p-value = 0.001). Humidity and Rainfall were not significant in the adjusted model. Conclusion: Temperature is among the effective climatic parameters on the incidence of malaria which should be considered in planning for control and prevention of the disease.