Elimination of schistosomiasis as a public health problem and interruption of transmission in selected areas are key goals of the World Health Organization for 2025. Conventional parasitological methods are insensitive for the detection of light-intensity infections. Techniques with high sensitivity and specificity are required for an accurate diagnosis in low-transmission settings and verification of elimination. We determined the accuracy of a urine-based up-converting phosphor-lateral flow circulating anodic antigen (UCP-LF CAA) assay for Schistosoma haematobium diagnosis in low-prevalence settings in Zanzibar, Tanzania. A total of 1,740 urine samples were collected in 2013 from children on Pemba Island, from schools where the S. haematobium prevalence was <2%, 2–5%, and 5–10%, based on a single urine filtration. On the day of collection, all samples were tested for microhematuria with reagent strips and for the presence of S. haematobium eggs with microscopy. Eight months later, 1.5 ml of urine from each of 1,200 samples stored at -20°C were analyzed by UCP-LF CAA assay, while urine filtration slides were subjected to quality control (QCUF). In the absence of a true ‘gold’ standard, the diagnostic performance was calculated using latent class analyses (LCA). The ‘empirical’ S. haematobium prevalence revealed by UCP-LF CAA, QCUF, and reagent strips was 14%, 5%, and 4%, respectively. LCA revealed a sensitivity of the UCP-LF CAA, QCUF, and reagent strips of 97% (95% confidence interval (CI): 91–100%), 86% (95% CI: 72–99%), and 67% (95% CI: 52–81%), respectively. Test specificities were consistently above 90%. The UCP-LF CAA assay shows high sensitivity for the diagnosis of S. haematobium in low-endemicity settings. Empirically, it detects a considerably higher number of infections than microscopy. Hence, the UCP-LF CAA employed in combination with QCUF, is a promising tool for monitoring and surveillance of urogenital schistosomiasis in low-transmission settings targeted for elimination. 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.