Malnutrition among primary school-age children has continued to pose a major public health issue, especially in developing countries. Nigeria is ranked amongst the top ten countries with the highest prevalence of undernutrition in children while about 2,300 children die daily in Nigeria as a result of malnutrition. Hence, the study was conducted to determine and compare the prevalence of malnutrition among public school pupils in rural and urban communities in Warri South LGA. This school-based comparative cross-sectional study made use of a bio-data form that collected socio-demographic details and anthropometric measurements of the pupils. The nutritional status of the pupils was obtained using WHO AnthroPlus software, while the resulting data were analysed and presented accordingly. The result showed that a total of 330 pupils (165 each from urban and rural public primary schools) were recruited, out of which more of the pupils in urban areas were younger, had parents who were better educated and employed while those from rural areas had higher family sizes. However, there was no difference in the sex and type of family of the pupils. The prevalence of malnutrition was reported as 36.7% with the prevalent form of malnutrition discovered as underweight (35.0%), followed by stunting (13.9%), overweight/obese (8.5%), and wasting (7.2%). Wasting, stunting, and overweight were higher among urban pupils, while the rate of underweight was higher among rural children. This high prevalence of undernutrition among urban pupils could be attributed to poor nutrition arising from a myriad of interrelated circumstances such as poor feeding, eating practices, and recurrent infection. Hence, the need for improved sensitisation of mothers concerning correct childhood feeding and provision of balanced nutrition.