Introduction: Anaemia remains a significant public health issue among schoolaged children in the Philippines, with multifactorial rural–urban disparities and limited evidence on their determinants. To address this gap, this study examined prevalence of anaemia and identified its key determinants among Filipino schoolaged children in rural and urban communities. Methods: A secondary analysis of 5,173 school-aged children from 2018–2019 Expanded National Nutrition Survey (ENNS) examined data on biochemical, socioeconomic, anthropometric, food security, and participation in government programmes. Multivariate logistic regression analysis was conducted separately by place of residence to identify the determinants of anaemia. Results: National prevalence of anaemia was 16.6%, classified as a mild public health concern according to World Health Organization (WHO) criteria, with significantly higher prevalence in rural areas (18.5%) compared with urban areas (13.7%). Overweight and obesity were consistently associated with lower odds of anaemia across settings (national, rural, and urban). At the national level, key determinants included education of household head, sanitation, and non-participation in dietary supplementation programmes. In rural areas, limited education among household heads and poor sanitation were dominant predictors. In contrast, in urban areas, male sex, stunting, underweight, and non-participation in dietary supplementation programmes were influential factors. Conclusion: Anaemia among Filipino school-aged children reflects complex interplay of nutritional, socioeconomic, environmental, and programme-related factors, with distinct determinants observed between rural and urban settings, highlighting the need for setting-specific interventions.