Japanese encephalitis virus (JEV) is a zoonotic pathogen that is maintained by mosquito vectors and vertebrate hosts including birds in a natural transmission cycle. Domestic ducklings are sensitive to JEV infection, but the clinical responses of domestic ducklings to natural JEV infection are unknown. In this study, we simulated the natural JEV infection of domestic ducklings via JEV-infected mosquito bites to evaluate the pathogenicity of JEV in domestic ducklings. Specific pathogen-free domestic ducklings were infected at day 2 post-hatching with JEV-infected Culex pipiens mosquito bites and monitored for clinical responses. Among 20 ducklings exposed to JEV-infected mosquitoes, six showed mild and non-characteristic clinical signs starting at two days post-infection, then died suddenly with neurological signs of opisthotonos (a condition of spasm of the back muscles causing the head and limbs to bend backward and the trunk to arch forward) between two and three days post-infection. The mortality of the affected ducklings was 30% (6/20). Multifocal lymphohistiocytic perivascular cuffs and lymphohistiocytic meningitis were macroscopically observed in the affected duckling brains. JEV was detected in the cytoplasm of neuronal cells in the affected duckling brains by immunohistochemical assays and was recovered from the affected duckling brains by viral isolation. These observations indicated that JEV infection via mosquito bites causes mortality associated with viral encephalitis in newly hatched domestic ducklings, thus demonstrating the potential pathogenicity of JEV in domestic ducklings under natural conditions.