BACKGROUND: After two decades of mass drug administration (MDA) for schistosomiasis in Burkina Faso, an impact assessment was conducted in 16 health districts (HDs) between February 2023 to March 2024 to determine the epidemiological situation of schistosomiasis in school-aged children and facilitate the decision for sub-district level treatment decision. METHODOLOGY/PRINCIPAL FINDINGS: A cross-sectional cluster survey was conducted with randomly selected children aged 5-14 years. Haemastix reagent strips were used to detect microhaematuria in urine, and urine filtration was used to detect and quantify Schistosoma haematobium eggs in children with microhaematuria. The Kato-Katz was used to detect and quantify S. mansoni eggs in fecal samples. The prevalence of infection and the prevalence of heavy-intensity (HI) infections were calculated. The overall prevalence of schistosomiasis was 2.4% (range: 0-11.1%) in 16 HDs, with the overall prevalence of HI infection of 0.9% (range: 0-4.2%). Four HDs (Tenkodogo, Batié, Sig-Nonghin, and Karangasso-Vigué) had a prevalence of HI infection from 1.3% to 4.2%. Forty-seven health areas still had an overall prevalence of 1.4-62.5%, with seven health areas in five HDs >
10%, and 29 health areas had a prevalence of HI infection from 1.4% to 22.9%. Boys had a higher prevalence of HI infections than girls. The prevalence of microhaematuria at 5.8% was significantly higher than that of S. haematobium infection by urine filtration at 2.3%, and Haemastix results were significantly associated with the intensity of infection. CONCLUSIONS/SIGNIFICANCE: The results showed that progress has been made in eliminating schistosomiasis as a public health problem in the 16 HDs in Burkina Faso after two decades of mass treatment. However, hotspots of infections remain, with 29 health areas having a prevalence of HI infection above the 1% threshold. The results provide evidence for planning targeted sub-district-level treatment.