Over the last few decades, stunting has decreased worldwide, although the prevalence remains high in underdeveloped and developing countries. A child's healthy growth is a key measure of their overall well-being, and it is directly linked to his or her nutrient intake and resistance to illnesses. This study determined the nutrient intake of stunted Filipino school-age children utilizing secondary data from the 2018–2019 Expanded National Nutrition Survey conducted by the Department of Science and Technology–Food and Nutrition Research Institute. A total of 26,332 5–10-yr-old school-age children were included in the study. The data utilized were nutritional status, socio-economic status and demographic profile, and nutrient intake of school- age children. Stata version 16 was used for all statistical tests, whereas the PC-SIDE software was used for the estimation of the mean usual intake of energy and nutrients. Among stunted school-age children, mean energy, protein, iron, thiamin, riboflavin, niacin, and fat intake were significantly higher among urban households than their counterparts. The proportion of stunted school-age children meeting the recommended intake for energy (9.3%), iron (15%), vitamin A (24.8%), thiamin (27%), and riboflavin (29.8%) were significantly higher in the urban as compared to rural areas. The energy, protein, vitamin A, vitamin C, thiamin, niacin, riboflavin, iron, and calcium intake of stunted school-age children were significantly lower as compared to the non-stunted. The data show that despite the decreasing prevalence of undernutrition in the country, the problem of childhood stunting still persists. Furthermore, non-stunted children only had slightly better nutrient intakes. These urges work on the major determinants of stunting in the Philippines and the implementation of appropriate interventions such as supplementary feeding programs, food production, and nutrition education.