BACKGROUND: Hookworm infection and schistosomiasis are two of sub-Saharan Africa's most common neglected tropical diseases. An annual mass drug administration (MDA) program against schistosomiasis and soil-transmitted helminths (STHs), including hookworm, has been implemented in Mayuge district, Uganda, since 2003 to date. However, hookworm and schistosomiasis remain prevalent in Mayuge district. Understanding the factors that predispose children to these infections in the context of MDA could inform interventions to reduce prevalence in Uganda and similar settings. METHOD: This cross-sectional study took place in 33 randomly selected primary schools in the Mayuge district from January to February 2022. Children in primary classes 4 or 5, in the selected schools provided single stool samples and completed questionnaires. Stool specimens were examined using the Kato-Katz method to determine the prevalence of hookworm and schistosomiasis. We performed univariable and multivariable logistic regression to assess the associations of each infection with potential risk factors. RESULT: A total of 1,617 students (mean age 12.1 years, 50.1% male) were enrolled. The prevalence of hookworm infection and schistosomiasis was 21.8% (95% confidence interval (CI): 19.8-23.9%) and 18.7% (95% CI: 16.8-20.7%), respectively. In multivariable analysis, longer water fetching time (over 30 min versus less than 30 min) and working daily in the soil were associated with increased odds of hookworm infection (adjusted odds ratio (AOR): 1.49, 95% CI: 1.13-1.96 and 1.37, 95% CI: 1.03-1.82, respectively). Higher odds of schistosomiasis were linked to proximity to water bodies within a one-hour walking distance (AOR: 1.84, 95% CI: 1.35-2.50), and not always washing hands before eating (AOR: 2.00, 95% CI: 1.50-2.67). Swimming, bathing, or washing in water bodies twice a week, compared to never, also increased schistosomiasis odds (AOR: 2.91, 95% CI: 1.66-5.13). CONCLUSION: Consistent with the mechanisms of acquisition, hookworm infection increased with exposure to soil, and schistosomiasis increased with exposure to unclean water. Our findings highlight the importance of Water, Sanitation, and Hygiene programs and strategies aimed at reducing exposure within the framework of Neglected Tropical Disease elimination programs.