This study aimed to assess the prevalence and identify risk factors of schistosomiasis among school-aged children in low- and middle-income communities. A retrospective cross-sectional study was conducted to review patient records of school-age children. Data on gender, age, sub-district, area residing in, patient status, history of bilharzia, presence of blood in the urine, and schistosomiasis diagnoses were collected. The data were analyzed using IBM Statistical Package for the Social Sciences (SPSS) version 27. Logistic regression was employed to determine the factors associated with schistosomiasis. The overall prevalence of schistosomiasis in the study population was 75%, with higher prevalence observed among male children (89%), children aged between 10 and 14 years (59%), urban areas (51%), and rural-dominated districts, particularly Bushbuckridge (42%) and City of Mbombela (51%). Age, especially 10–14 years old (p ˂ 0.01; 95%CI: 1.98–2.29), a history of bilharzia (p = 0.01; 95%CI: 1.15–1.96), and the presence of blood in urine (p ˂ 0.01; 95%CI: 2.02–2.40) were significantly associated with schistosomiasis while being a female child was found to be a protective factor (AOR: 0.35; CI 0.35–0.41). This study underscores the importance of implementing robust screening procedures and the necessity for health education to mitigate the high prevalence of schistosomiasis and prevent its further spread.