Objectives The aim of this study was to investigate dietary intakes and nutritional status among Uganda primary school children from two selected schools in urban and rural areas. Methods Data were collected from 350 pupils (6-14 years) in Mpigi district, Uganda. All participants were offered a school lunch meal (usually maize porridge and boiled beans). Dietary survey was conducted in October 2016. Data for dietary intake levels were collected by the 24-hour recall method with trained school staffs. The data were converted into nutrient intakes using the CAN-Pro 5.0 Program and compared with KDRIs to evaluate the nutritional status of the subjects. Diet quality indexes such as nutrient density, nutrient adequacy ratio (NAR), mean adequacy ratio (MAR), and index of nutritional quality (INQ) and a diet diversity index such as diet diversity score (DDS) were calculated to evaluate nutritional status among subjects. Data were analyzed using SPSS statistical programs. Results Results show that the intakes of most nutrients were significantly different by schools. The nutritional status of micro-nutrients was very low in both schools according to analysis of nutritional indexes such as NARs and INQs. Students from both schools should improve intakes of micro-nutrients related to child growth such as calcium, Vitamin B6, zinc and folate. According to the analysis of dietary diversity, there was difference in dietary patterns by schools presumably due to their locations. Conclusions This suggests that current meals could not provide adequate nutrients for the subjects and urgent nutrition interventions for school food services are needed to improve their nutritional well-being. New foods supplements based on local cuisine are also needed to ensure dietary diversity and sustainable development plans.