Background: The application of anthropometric measurement which entails assessing the nutritional status (stunting, wasting, obesity, overweight, and underweight) of children, is an essential part of monitoring the health of a community. Aim: To investigate and compare the anthropometric indices of nutritional status among public school pupils in rural and urban communities in Warri South LGA. Materials and Method: This comparative cross-sectional study made use of a pretested interviewer-administered questionnaire while the nutritional status of the pupils was obtained using WHO AnthroPlus software. The resulting data were analysed and presented accordingly. Results: The result showed that there were slightly more males (50.9%) than females (49.1%), while urban pupils were younger than their rural counterparts. Also, the mean scores for the weight, WAZ, Height, HAZ and BAZ were 26.67±5.77, -0.96±1.49, 1.32±0.10, -0.43±1.55 and -0.67±1.13 respectively, while there was no statistically significant (p>0.05) relationship between these anthropometric variables and the sex of the pupils. However, urban pupils had a statistically significant (p<0.05) higher weight and height in comparison with their rural counterparts who on the other hand had statistically significant (p<0.05) higher HAZ and BAZ which translates to a higher amount of wasting and stunting among the urban pupils Conclusion: Children in urban primary schools are taller and fatter but more stunted and wasted. Hence, appropriate nutritional education programmes should be initiated for pupils, parents, and teachers, while more efforts should be made to improve the current school feeding program.