In this paper, we describe the fabrication of a paper-based enzyme-linked immunosorbent assay (ELISA) to detect polygalacturonase (PG), which is used as a biomarker to determine whether a plant is infected with a disease. The proposed paper-based ELISA can analyze the concentration of PG in a short time using a small sample compared to the traditional ELISA, which is generally performed using a well plate. To increase the resolution of the sensor, we optimized the dilution ratio of the HRP-conjugated goat anti-rabbit IgG antibodyand the dilution ratio of the anti-PG and HRP-conjugated goat anti-rabbit IgG antibodies. Furthermore, for quantitative analysis of PG concentration, Delta RGB analysis was conducted to detect color changes in the sensing window displayed by the PG samples at various concentrations. Based on the experiment, the fabricated paper-based ELISA could measure at least 0.25 µg of PG and the measurement range was 0.25–2 µg. Therefore, the paper-based ELISA for detecting PG is expected to be able to determine the presence or absence of disease in crops at the infection stage in the future.