Following implementation of the national control program, a reassessment of Schistosoma mansoni prevalence was conducted in Burundi to determine the feasibility of moving toward elimination. A countrywide cluster-randomized cross-sectional study was performed in May 2014. At least 25 schools were sampled from each of five eco-epidemiological risk zones for schistosomiasis. Fifty randomly selected children 13-14 years of age per school were included for a single urine-circulating cathodic antigen (CCA) rapid test and, in a subset of schools, for duplicate Kato-Katz slides preparation from a single stool sample. A total of 17,331 children from 347 schools were tested using CCA. The overall prevalence of S. mansoni infection, when CCA trace results were considered negative, was 13.5% (zone range [zr] = 4.6-17.8%), and when CCA trace results were considered positive, it was 42.8% (zr = 34.3-49.9%). In 170 schools, prevalence of this infection determined using Kato-Katz method was 1.5% (zr ==0-2.7%). The overall mean intensity of S. mansoni infection determined using Kato-Katz was 0.85 eggs per gram (standard deviation = 10.86). A majority of schools (84%) were classified as non-endemic (prevalence = 0) using Kato-Katz; however, a similar proportion of schools were classified as endemic when CCA trace results were considered negative (85%) and nearly all (98%) were endemic when CCA trace results were considered positive. The findings of this nationwide reassessment using CCA rapid test indicate that Schistosoma infection is still widespread in Burundi, although its average intensity is probably low. Further evidence is now needed to determine the association between CCA rapid test positivity and low-intensity disease transmission.