The present study evaluated the paraprobiotic effect of heat-inactivated Bacillus amyloliquefaciens FPTB16 on immunological response and immune relevant gene expression in catla (Catla catla). Heat inactivation of viable cells of B. amyloliquefaciens was done at 60 °C for 2 h. For preparation of paraprobiotic supplemented diet, the heat-inactivated bacteria were added to the basal diet (control) at three different inclusion levels i.e., 107, 108 and 109 cells g−1 diet. Fish (25.98 ± 2.57 g) were fed with these diets and various immune responses and immune relevant gene expressions were measured after 4 weeks of feeding. Biochemical parameters were also measured along with the immunological responses. Immunological parameters viz. oxygen radical production, serum lysozyme activity and total serum protein content showed significant enhancement (p < 0.05) in fish fed with 108 and 109 cells g−1 diet. Significant enhancement in myeloperoxidase activity was observed in all the dietary groups compared to control. Alkaline phosphatase activity showed significant enhancement (p < 0.05) in fish fed with 107 and 108 cells g−1 diet. Biochemical parameters viz. GPT, GOT and glucose content did not show any significant difference in any of the dietary groups. Immune relevant genes viz. IL-1β, TNF-α, C3 and iNOS showed significantly higher expression in either liver or head-kidney tissues in most of the cases. However, IFN-γ expression showed a down-regulation pattern in both the tissues. In conclusion, the dietary supplementation of heat-inactivated B. amyloliquefaciens enhanced the immunity of catla, particularly at 108 cells g−1 diet. The results collectively suggest the paraprobiotic applicability of B. amyloliquefaciens in aquaculture.