A sudden drop in egg production in commercial poultry flocks can be economically devastating, and rapid identification of the cause often requires a combined effort between the producer, veterinarian, and pathologist. In September 2019, a 35-wk-old commercial Pekin breeder duck flock in Indiana suffered a drop in egg production from 1700 to 1000 eggs daily (41.2% drop). Again, in September 2021, three Pekin breeder duck flocks aged 32, 58, and 62 wk from the same company suffered a similar drop in egg production, with a mild increase in weekly mortality of 1.0% to 2.5%. In 2019 and in 2021, birds from affected flocks were submitted to the Veterinary Diagnostic Laboratory at Michigan State University for postmortem examination. Common gross examination findings included flaccid, shrunken, or atrophied ova (all hens), pododermatitis, airsacculitis, hepatomegaly, splenomegaly, ascites, and pallor of the left ventricle. Histopathologic examination of cerebrum, cerebellum, and brainstem revealed mild lymphocytic perivascular cuffing, vasculitis, and gliosis, suggesting viral encephalitis. In the heart, there was mild multifocal cardiomyocyte necrosis, mineralization, and infiltration by lymphocytes and macrophages. PCR for Newcastle disease virus, avian influenza virus, eastern equine encephalitis virus, and West Nile virus (WNV) was performed. Brain and heart samples were positive for WNV by PCR, and WNV antigen was detected in the cerebellum by immunohistochemistry. This is the first report to associate WNV infection with a drop in egg production in waterfowl, which are known to be important reservoir species for WNV and, as such, are generally asymptomatic.