Malaria is a leading cause of morbidity and mortality among children, particularly in sub-Saharan Africa. Although substantial progress has been made in the treatment of pediatric malaria with artemisinin-based combination therapy, there remain many obstacles to the effective implementation of these highly efficacious new treatment options. Similarly, while effective tools are available for the prevention of malaria in children, scaling these up so that they have a clear impact on malaria-associated morbidity and mortality has presented significant challenges to public health officials. Host nutritional status influences the acquisition and potential severity of malaria infection. While there is substantial evidence that malaria contributes to impaired weight and height gain in children, the impact of undernutrition on malaria is complex. There is increasing evidence that supplementation with certain micronutrients may play a critical role in the prevention of malaria in young children. Micronutrient interventions such as zinc or vitamin A supplementation may help reduce the burden of disease due to malaria whereas others such as iron may exacerbate infection. Differences in study design, quality, intensity of malaria transmission, and other study site characteristics complicate the interpretation of the limited number of studies that have evaluated the impact of specific micronutrients for the treatment and prevention of malaria. There has only been one trial to evaluate the use of zinc as an adjunct in the treatment of malaria and it failed to demonstrate any benefit of zinc in this role. This article reviews the clinical management of malaria in children, interactions between malaria and nutritional status, and the potential role of micronutrient supplementation for the prevention of clinical malaria episodes in young children, with a particular focus on whether each nutrient supplement improves or worsens malaria outcomes.