Japanese encephalitis infection is a vector-borne disease caused by the flavivirus Japanese encephalitis virus (JEV). It is responsible for severe brain infections in humans worldwide. Given the ubiquitous nature of complications and tropism associated with Japanese encephalitis (JE) infection, a holistic understanding of its molecular mechanism is essential. The phenomenon of abnormal protein aggregation into pathogenic amyloids is now increasingly linked to multiple human diseases, also known as Amyloidosis. Most are neurodegenerative disorders, but amyloidosis is not restricted to a specific organ or tissue type. The overlap of viral protein aggregation with human pathologies remains limited, and it is gaining momentum, especially after the devastating Covid-19 pandemic. Therefore, in this study, we have examined the likelihood of aggregation for the entire collection of proteins in JEV. Multiple independent web server tools were employed to scan for potential amyloid-prone regions (APRs), and it was followed by in vitro validation using two JEV transmembrane domains, Capsid anchor, and 2K peptides. These synthetic viral peptides were introduced to artificial aggregation-inducing conditions and then analyzed using different dye-based assays and microscopy methods confirming amyloid-like fibril structure formation. We found these aggregates cytotoxic to human neuronal cell lines and membrane damaging to human blood-derived RBCs. The aggregation kinetics of both peptides is enhanced in the presence of artificial membrane models and seeds of self and diabetes hallmark protein Amylin. Our findings thereby strongly suggest the possibility of JEV protein aggregation playing a vital role in its pathogenesis, opening up a broad scope of future study. Also, the interplay between JEV protein aggregation and initiation/progression of other proteopathies is possible and needs further exploration.