Malaria hazard has become a major public health problem especially in the sub-Saharan African regions and Nigeria in particular. While malaria cases decrease globally in recent times, it increases exponentially in Nigeria resulting in many deaths especially among children under five years. This study examined historical trend and anomaly of malaria cases and mortality in Nigeria spanning a period of sixty years. The result shows that malaria prevalence increased significantly between 2000 and 2015 and most of the cases were found among children and women. It was also found that malaria distribution in Nigeria may experience a shift towards the north central region due to complex environmental, social and demographic factors. The observed shift in parasite prevalence across regions in the country suggests that more studies on climate change impacts on malaria transmission within the country should be carried out.