This study sought to investigate prevalence of urogenital and intestinal schistosomiasis among school age children 6–13 years in selected communities in the Okavango Delta. The termination of the Botswana national schistosomiasis control program in 1993 contributed to its neglect. An outbreak of schistosomiasis in 2017 at one of the primary schools in the northeastern part of the country resulted in 42 positive cases, indicating that the disease exists. A total of 1,611 school age children 6–13 years were randomly selected from school registers in 10 primary schools; from which 1603 urine and 1404 stool samples were collected. Macroscopic examination of urine and stool for color, odor, blood; viscosity, consistency, and the presence of worms. Urine filtration and centrifugation methods were used to increase sensitivity of detecting parasite ova. Kato-Katz and Formalin-Ether were used for the examination of stool samples. Data were analyzed using SPSS version 25. Results were expressed as odds ratio (OR) with their 95% CI and statistical significance set at p < 0.05. A total of (n = 1611) school age children 6–13 years participated in the study, mean age 9.7years (SD 2.06), females (54%) and males (46%). Results indicated an overall prevalence ofSS.hematobiumandS.mansoniat 8.7% and 0.64% respectively. Intensity ofSS.hematobiumwas generally light (97.6%) and heavy intensity (2.4%). Results also revealed a knowledge deficit, about 58% of children had never heard of bilharzia even though they lived in communities where the disease was previously endemic. Learners who had a family member who previously suffered from schistosomiasis had higher knowledge than those who did not. Interestingly, these learners were likely to engage in risky behaviors compared to those with lower knowledge of the disease. An integrated approach that emphasizes health education, mass drug administration, water, sanitation, and hygiene infrastructure should be prioritized for prevention and control of schistosomiasis.