The study examines the population-level impact of temperature variability and immigration on malaria prevalence in Nigeria, using a novel deterministic model. The model incorporates disease transmission by immigrants into the community. In the absence of immigration, the model is shown to exhibit the phenomenon of backward bifurcation. The disease-free equilibrium of the autonomous version of the model was found to be locally asymptotically stable in the absence of infective immigrants. However, the model exhibits an endemic equilibrium point when the immigration parameter is greater than zero. The endemic equilibrium point is seen to be globally asymptotically stable in the absence of disease-induced mortality. Uncertainty and sensitivity analysis of the model, using parameter values and ranges relevant to malaria transmission dynamics in Nigeria, shows that the top three parameters that drive malaria prevalence (with respect to [Formula: see text]) are the mosquito natural death rate ([Formula: see text]), mosquito biting rate ([Formula: see text]) and the transmission rates between humans and mosquitoes ([Formula: see text]). Numerical simulations of the model show that in Nigeria, malaria burden increases with increasing mean monthly temperature in the range of 22–28[Formula: see text]. Thus, this study suggests that control strategies for malaria should be intensified during this period. It is further shown that the proportion of infective immigrants has marginal effect on the transmission dynamics of the disease. Therefore, the simulations suggest that a reduction in the fraction of infective immigrants, either exposed or infectious, would significantly reduce the malaria incidence in a population.