Background: Malaria remains the leading cause of morbidity and mortality among children in sub-Saharan Africa, yet fine-scale geospatial data on its distribution and environmental determinants at the primary care level are scarce in the Federal Capital Territory (FCT), Abuja, Nigeria. This study mapped the geospatial distribution of malaria prevalence across all six area councils of the FCT and identified environmental determinants of malaria risk among children attending primary health care (PHC) facilities. Methods: A cross-sectional analytical study was conducted from October to December 2025 across 12 PHC facilities in six area councils of the FCT. A total of 385 children were enrolled using multi-stage sampling. Malaria diagnosis was performed by both rapid diagnostic test (RDT) and light microscopy. Environmental conditions was divided into household and peridomestic environmental risk factors were assessed using structured questionnaires. Geospatial analysis employed kernel density estimation (KDE) and Getis-Ord Gi* statistics using QGIS 3.28 and Python. Binary logistic regression identified independent predictors of malaria positivity. Results: Overall RDT-confirmed malaria prevalence was 38.4% (148/385; 95% CI: 33.5–43.4%) and microscopy prevalence was 32.2% (124/385). Significant spatial heterogeneity was observed: Abaji area council recorded the highest prevalence (RDT: 48.4%; microscopy: 50.0%) and was confirmed as a primary hotspot by Getis-Ord Gi* analysis; Kwali was a secondary hotspot (42.2%); and Gwagwalada had the lowest burden (29.7%). Significant temporal decline from October (58.3%) to December (22.5%) was documented (χ²=37.039, p<0.0001). None of the household factors were statistically significant However among peridomestic environmental factors, stagnant water (p=0.005), nearby bushes (p=0.004), gutters (p=0.042), car tyres (p=0.009), and abandoned containers (p=0.016) were all significantly associated with higher malaria prevalence. Compound