-Intestinal protozoan infections remain a significant public health issue, causing over 800 million cases and 4.5 million deaths annually, particularly in regions with poor sanitation, low socioeconomic conditions, and limited access to safe drinking water. This study aims to determine the prevalence and factors associated with intestinal protozoan infections among children under 10 years of age in the Kibogora Level Two Teaching Hospital (hereafter referred to as Kibogora Hospital) catchment area, Nyamasheke District, in 2023. An analytical cross sectional study was conducted to assess these factors. Data was collected by the researcher and trained data collectors (nurses) from a sample size of 384 children under 10 years who were attending the Kibogora Hospital catchment area. A proportional stratified random sampling method was used to select the participants. Data were collected using a structured questionnaire and laboratory tests. The questionnaire gathered information on patient demographics and risk factors, while laboratory tests identified the presence of protozoan infections. The collected data was entered into an electronic SPSS version 25.0 data sheet for further analysis. For categorical variables, bivariate analysis, chi-square tests, and multiple logistic regression analysis were performed. Variables with a p-value of less than 0.05 at a 95% confidence interval were considered significant. The findings were presented in tables and charts. The Kibogora Hospital Administration granted authorization to conduct this research upon receipt of the application letter from Mount Kenya University. The study's findings revealed that Figure 4.1 illustrates that 24.5% of the children in the study tested positive for intestinal protozoan infections, while the majority, 75.5%, tested negative. The multivariate data analysis showed that children whose parents have not received an education are at a markedly increased risk of protozoan infections, with an adjusted odds ratio (AoR) of 5.171 (95% CI: 1.982–13.491, p = 0.001). Children receiving care from Cyivugiza or Ngange health centers exhibit a significantly higher likelihood of infection (AoR = 2.632, 95% CI: 1.231–5.629, p = 0.01). Hygiene training provided by health workers emerges as another critical factor, with untrained caregivers presenting a higher risk of infection (AoR = 3.030, 95% CI: 1.647–5.575, p < 0.001). The lack of child handwashing practices also demonstrates a significant association with infection rates. Those who do not wash their hands before eating are 4.041 times more likely to have protozoan infections (95% CI: 2.133–7.657, p < 0.001), while not washing hands after using the toilet raises the odds to 2.874 (95% CI: 1.588–5.202, p < 0.001). In addition, the use of compost for waste disposal is strongly linked to reduced infection rates (AoR = 7.076, 95% CI: 3.391–14.764, p < 0.001), emphasizing the potential impact of effective waste management strategies. In conclusion, the study reveals that nearly one-quarter of the children were infected with protozoan parasites and a lot of factors contribute to protozoan infections in young children, lack of mother’s education, healthcare access, hygiene training, and unproper waste disposal practices being key areas for intervention to improve child health outcomes in the Kibogora region. The study recommends implementing educational programs to expand child health services.