Enzyme-linked immunosorbent assay (ELISA) is a new approach for the diagnosis of Opisthorchis viverrini antigen (OvAg) in urine samples. Herein, we demonstrate a portable fluorometer based on the smartphone to use as the point-of-care device for the diagnosis of OvAg in urine samples by fluorescence ELISA. In addition, the detection sensitivity of the fluorescent assay has been improved by a simple strategy using aqueous micelles of the non-ionic surfactant. The combination of a smartphone-based device with fluorescent enhancement provides an excellence tool for the diagnosis of the OvAg in urine samples. The smartphone-based device shows excellent potential for measuring the fluorescence signal comparable with a fluorescence microplate reader. The signal in the green channel (G) of the smartphone representing the emission intensity from the fluorescence ELISA exhibits a good linear relationship with OvAg concentration with an LOD of 33 ng mL−1. The proposed device achieved high diagnostic sensitivity, specificity, and accuracy of 84.88%, 89.66%, and 86.14%, respectively, compared to the measurement by conventional instruments (colorimetric ELISA). The smartphone-based device has been verified for the diagnosis of OvAg in urine samples from an endemic area with excellent results. Therefore, smartphone-based diagnostics is an effective point-of-care device for on-site assay of OvAg detection in urine samples.