The World Health Organization aspires to eliminate snail fever (schistosomiasis) as a public health problem and to interrupt the transmission of this disease in selected areas by 2025. Efforts to achieve these goals are currently being intensified. As a result, the prevalence and intensity of infection will decline in many parts of the world. To detect light-intensity infections, diagnostic tools with a high sensitivity and specificity are needed. We assessed the accuracy of a method that is able to diagnose schistosomiasis via the detection of circulating anodic antigen (CAA) in urine. We examined 1,200 urine samples from children living on Pemba Island, Tanzania, a low-endemic area targeted for schistosomiasis elimination. We found that the CAA-test had a considerably higher sensitivity than conventional urine filtration microscopy and reagent strips that are widely used in schistosomiasis control programs. The empirical prevalence of infection with the parasite Schistosoma haematobium determined by the CAA-test was up to 10 times higher than that obtained by urine filtration. Our results suggest that the CAA-test—in combination with urine filtration—is a promising approach for the diagnosis of S. haematobium in low-transmission settings that are targeted for elimination.