Palmitoylation, a reversible post-translational modification, is initiated by the DHHC family of palmitoyltransferases. Nevertheless, the function and mechanisms of protein palmitoylation in the context of JEV infection remain unclear. This study demonstrates that palmitoyltransferases (PAT) DHHC21 plays a pivotal role in the enhancement of JEV replication. By means of immunoprecipitation-mass spectrometry (IP-MS), the target protein of DHHC21 was identified as HSPA8. Moreover, the DHHC21-HSPA8 interaction was validated through the utilisation of co-immunoprecipitation (CO-IP) and immunofluorescence (IF) assays. Acyl-PEGyl exchange (APE) experiments demonstrated that DHHC21 is capable of catalyzing the palmitoylation modification of HSPA8 at the 574 Cys site. And modification site can result in a reduction in the half-life of HSPA8 and a concomitant decrease in protein content. These findings elucidate the influence of palmitoylation modification on JEV replication and augment our comprehension of JEV infection pathogenesis.