West Nile virus infection is more frequently associated with neuroinvasive disease and high morbidity and mortality in immunocompromised hosts. Here, we describe a 47-year-old Egyptian kidney transplant recipient who was admitted to our department in 2016 for persistent fever, altered mental status, and upper limb tremors. In addition, renal impairment, signs of acute thrombotic microangiopathy, pancreatitis, and slightly altered inflammatory indices were present. The patient was treated with antibacterial and antiviral therapy, and reduced immunosuppressive therapy was prescribed. After several biochemical and instrumental examinations, only slight blood positivity for West Nile virus immunoglobulin M in the absence of immunoglobulin G was found, whereas immunoglobulins M and G on cerebrospinal fluid and West Nile virus polymerase chain reaction were negative. Serology evaluated after 23 days of hospitalization confirmed immunoglobulin M positivity and detected weak immunoglobulin G positivity; however, according to the US Centers for Disease Control and Prevention diagnostic criteria, it was not sufficient to confirm diagnosis. During hospitalization, clinical recovery was observed, but severe renal insufficiency persisted. Renal biopsy performed after clinical recovery demonstrated chronic antibody-mediated rejection with advanced chronic lesions, without viral cytopathic signs. Four months later, we received confirmation of West Nile virus infection by plaque reduction neutralization test. The current case described severe West Nile virus infection with clinical neurologic involvement, thrombotic microangiopathy, and pancreatitis, resulting in irreversible loss of kidney function. Delayed diagnosis, based on US Centers for Disease Control and Prevention criteria, was due to absence of both characteristic radiologic features and sensitive and promptly available laboratory tests. This case stresses the need for accurate diagnostic tests and/or a partial revision of the diagnostic criteria. In fact, with an earlier diagnosis, we would have avoided diagnostic and therapeutic procedures that may have contributed to the loss of graft function in the described case.