Although waterfowl are less susceptible to Newcastle disease (ND) virus (NDV) infection compared with chickens and turkeys, lethal ND in waterfowl has been sporadically reported. Factors underlying the high pathogenicity of certain NDV strains in waterfowl remain unclear. In ducks, the NDV 9a5b isolate shows low pathogenicity while the d5a20b isolate shows high pathogenicity. This study aimed to identify the definitive lesions that led to the lethal virulence of d5a20b by comparing the histopathology of 9a5b- or d5a20b-inoculated ducks in order to elucidate lesions related to the enhanced pathogenicity of certain NDV strains in ducks. Herein, 7-day-old ducks were intranasally inoculated with either 9a5b or d5a20b NDV strains. The neurological signs were more severe in the d5a20b-inoculated group than in the 9a5b-inoculated group. Ducks in the d5a20b-inoculated group exhibited more severe lymphoid depletion in immune organs than those in the 9a5b-inoculated group, which may have caused an immunosuppressive state in the d5a20b-inoculated ducks. Ducks in the d5a20b-inoculated group had more severe nonsuppurative encephalitis with increased NDV nucleoprotein than those in the 9a5b-inoculated group. Additionally, pancreatic necrosis, with intralesional NDV nucleoprotein, was more severe in the d5a20b-inoculated group than in the 9a5b-inoculated group. Our results showed that the immune organs, brain, and pancreas were significant targets of the NDV d5a20b infection in ducks.