Despite continuous efforts to control schistosomiasis (SCH) in the Democratic Republic of the Congo (DRC), it still poses a significant challenge. In order to enhance control measures, additional research is necessary. This study documents the burden of SCH infection and its predictors in a rural area of the DRC. We conducted a household cross-sectional study from June to August 2021 among 480 school-aged children (SAC) aged 5–15 years living in a rural area of Kisangi, in the southwest DRC. We collected and examined stool, urine, and blood samples of each child. Additionally, we obtained data on anthropometry, socio-demographics, household information, and individual water contact behaviors. The overall prevalence of SCH infection was 55.8% (95% CI: 51.4–60.3), with prevalences of 41% (95% CI: 36.6–45.5), 36.3% (95% CI: 31.9–40.6), and 38.4% (95% CI: 32.6–44.3) for S. haematobium and S. mansoni infections and both infections, respectively. Among those with SCH infection, most had a light (67.5%) or heavy (51.7%) infection intensity. The geometric mean egg count was 16.6 EP 10 mL (95% CI: 12.9–21.3) for S. haematobium and 390.2 EPG (95% CI: 300.2–507.3) for S. mansoni. However, age (10 years and above (aOR: 2.1; 95% CI: 1.5–3.1; p < 0.001)) was an independent risk factor for SCH infection. The overall prevalence of malaria infection was 16.9% (95% CI: 13.5–20.2), that of stunting was 28.7% (95% CI: 24.7–32.8), that of underweight was 17.1% (95% CI: 12.8–21.4), and that of thinness was 7.1% (95% CI: 4.8–9.4). Anemia was prevalent at 49.4% (95% CI: 44.9–5), and the median Hb level of all participants was 11.6 g/dL (IQR: 10.5–12.6 g/dL). Anemia was strongly associated with SCH infection (aOR: 3.4; 95% CI: 2.3–5.1; p < 0.001) yet there was no association with the risk for malaria infection (aOR: 1.0; 95% CI: 0.6–1.8; p = 0.563). In addition, the risk of anemia increased with heavy infection intensities (p < 0.026 and p < 0.013 for S. haematobium and S. mansoni, respectively). However, stunting had a protective factor for anemia (aOR: 0.3; 95% CI: 0.2–0.4; p < 0.001). To conclude, SCH infection was widespread among the SAC and strongly linked to anemia. These results provide evidence of the hyperendemicity of infection in the study area, which requires preventative measures such as chemotherapy to reduce the schistosomiasis-associated morbidity, and micronutrient supplements to avoid anemia.