Background/Purpose: Over the last two decades, malaria has remained a major worldwide public health concern, especially in the developing countries leading to high morbidity and mortality among children. Nigeria is the world most burdened malaria endemic nation, contributing more than a quarter of global malaria cases. This study determined the prevalence of malaria among children 6-59 months in Nigeria, and the effects of individual and contextual factors. Methods: The study utilized data from 2018 Nigeria Demographic and Health Survey (NDHS) involving a weighted sample size of 10,185 children who were tested for malaria using rapid diagnostic test (RDT). Given the hierarchical structure of the data set, such that children at level-1 are nested in community at level-2, and nested in states and Federal Capital Territory (FCT) at level-3, multilevel mixed effect logistic regression models were used for the analysis. Results: The proportion of children 6-59 months of age in Nigeria that had malaria fever positive as assessed by RDTs was 35.5% (3,418/10185), (CI: 33.9-37.1). Kebbi State had the highest proportion of children 6-59 months who were malaria positive, 77.6%, (CI: 70.2-83.5), followed by Katsina State, 55.5%, (CI: 47.7-63.1). The Federal Capital Territory (FCT), Abuja had the proportion of 29.6%, (CI: 21.6-39.0), malaria positive children of 6-59 months of age. Children between the age of 48 and 59 months were 2.68 times more likely to have malaria fever than children 6-11 months of age (AOR=2.68, 95% CI: 2.03-3.54). Also, children from the rural area (AOR= 2.12, 95% CI: 1.75-2.57), were more likely to suffer from malaria infection compare with children from urban area. Conclusion: The study identified some individual and contextual predictors of malaria among children in Nigeria. These factors are areas that need to be considered for policy designs and implementations toward control and total elimination of malaria-related morbidity and mortality among children in Nigeria.