The WHO guidelines for monitoring and evaluating Schistosoma mansoni control programs are based on the Kato-Katz (KK) fecal examination method; however, there are limitations to its use, particularly in low prevalence areas. The point-of-care urine circulating cathodic antigen (POC-CCA) assay has emerged as a useful tool for mapping schistosomiasis prevalence, but its use in monitoring and evaluating control programs has not been evaluated. Before POC-CCA can be used for these programs, it must be determined how previous guidance based on the KK method can be translated to the POC-CCA assay; furthermore, its performance in different endemicity settings must be evaluated. Urine and stool specimens were collected from students attending public primary schools in western Kenya before mass treatment with praziquantel at baseline (51 schools), year 1 (45 schools), year 2 (34 schools), and year 3 (20 schools). Prevalence and infection intensity were determined by the KK method and POC-CCA assay. Changes in prevalence and intensity were compared within the strata of schools grouped according to the baseline prevalence determined by the KK method (0-10%, > 10-20%, > 20%). The prevalence determined by the POC-CCA assay was higher than that determined by the KK method at all time points for all strata. The prevalence determined by the KK method decreased from baseline to 2 and 3 years, as did infection intensity (with one exception). A corresponding decrease was not always replicated by the POC-CCA assay results. The POC-CCA assay did not perform as expected, and the concordance of results of the two tests was poor. Furthermore, there are emerging concerns regarding the specificity of the POC-CCA assay. Therefore, it is impossible to translate historical data and programmatic guidelines based on the KK method results to the POC-CCA assay.