Vibrio vulnificus infection causes severe economic losses in Oreochromis niloticus aquaculture by inducing pro-inflammatory cytokines, that lead to inflammation and mortality. Omega-3 fatty acids, such as Docosahexaenoic acid (DHA) and Eicosapentaenoic acid (EPA), have been reported for their anti-inflammatory and antibacterial abilities in murine and zebrafish models. However, the anti-inflammatory and antibacterial functions of DHA and EPA in commercial aquaculture organisms such as Oreochromis niloticus remain unknown. The present study demonstrates antibacterial function and transcriptional modulation of inflammation-associated genes by DHA and EPA in Vibrio vulnificus infection in Oreochromis niloticus fish models. The administration of EPA or DHA improved the Oreochromis niloticus survival rate against Vibrio vulnificus infection. The induction of proinflammatory cytokines, Interleukin (IL)-1β, IL-6, Tumor necrosis factor (TNF)-α, and Toll-like receptor (TLR)-2 by Vibrio vulnificus was suppressed in fish that were administered DHA. Bacterial membrane disruption and the killing of Vibrio vulnificus by EPA and DHA was observed using SEM, TEM, and cytoplasm leakage studies. In silico analysis of the transcription profile in Ingenuity Pathway Analysis software showed that DHA may enhance anti-Vibrio vulnificus activity in Oreochromis niloticus via the activation of peroxisome proliferator-activated receptor α (PPARα) to inhibit nuclear factor kappa B and suppress hepatocyte nuclear factor 4 α (HNF4α). In summary, the results of the present study demonstrated that DHA and EPA reduce the severity of Vibrio vulnificus infection and increase the survival rate of Oreochromis niloticus.