Background Fever in under-five children (U5) is the commonest presenting complaint in general practice and mothers’ recognition is an entry point for fever treatment, including malaria. This study describes rural-urban disparity in fever prevalence in U5, mothers’ malaria knowledge, care-seeking, testing for malaria before antimalaria medication and the associated factors.Methods A cross-sectional survey was conducted among 630 mother-child pairs (rural (300) and urban (330)) selected randomly using a multi-stage sampling from 63 villages in Igabi LGA, Kaduna State, Nigeria. Trained female data collectors administered a pre-tested structured questionnaire to collect information on mother-child demographic profiles, malaria knowledge, fever episodes in birth order last child in two weeks prior to survey, blood testing before antimalaria use, and delayed care seeking defined as care sought for fever >48 hours of onset. Malaria knowledge was categorized into good, average, and poor if the final scores were ≥75th, 50th-74th, and <50th percentiles, respectively. Frequency, proportions, and odds ratio were calculated. Statistically significant was set at p-value <0.05. Results The median age (interquartile range) of rural mothers was 30 (IQR, 10) years compared to 27 (IQR, 6) years in urban. Of the 70.0% (441/629) U5 children with fever, 58.5% (258/441) were in rural settlements. A third of the mothers whose child had fever sought care. Mothers in rural settlements were 2.8 (adjusted OR: 2.8, CI: 1.8-4.2, p <0.01) times more likely to delay care-seeking for fever. Other significant factors were poor or no knowledge of malaria transmission, poor perception of malaria as a major health problem, and household size > 5. Also, mothers who had no formal education were four times likely to receive antimalaria medications without testing fever for malaria compared to their educated counterpart (adjusted OR: 4.0, 95% CI: 1.6-9.9, p <0.000).Conclusions Rural-urban disparities existed between fever prevalence in U5 children, care-seeking practices by their mothers, and factors associated with delayed care-seeking and testing the fever for malaria before antimalaria medication. Fever treatment for high impact malaria elimination in Nigeria needs a context-specific intervention rather than ‘one-size-fits-all’ approach.