Whereas fishmeal (FM) is a significant protein supply, its expensive cost has limited its diet use. Therefore, it is necessary to find affordable and accessible FM replacers. The potential of neem seed protein hydrolysate (NSPH) to replace FM protein in the Oreochromis niloticus, Nile tilapia diet was studied after two-month feeding trial. Fish (N = 200) of 27.17 ± 0.09 body weight were haphazardly distributed into five groups and fed on experimental diets having five substitution percentages with NSPH: 0% (control), 10%, 20%, 30%, and 40% (NSPH0, NSPH10, NSPH20, NSPH30, and NSPH40, respectively). Following the feeding experiment, the fish were challenged with Aeromonas veronii (1 × 107 CFU/mL) as a pathogenic bacterium. The results revealed that the growth parameters, growth hormone, digestive enzymes, and immune parameters (nitric oxide, complement 3, lysozyme, and phagocytic activity %) values were linearly (p < 0.01) augmented with all NSPH replacement groups as compared with NSPH0 group. Moreover, the NSPH40 group showed the highest expression of muscular insulinlike growth factor 1 and intestinal amino acids and peptide transporters genes, followed by the NSPH30 group, then the NSPH10 and NSPH20 groups. The splenic immune-related genes (phosphoinositide-3-kinase regulatory subunit 3b, toll-like receptors (TLR-2 and TLR-7), transforming growth factor-beta, interleukins (IL-10 and IL-1β), and tumor necrosis factor-alpha) and antioxidant-related genes (glutathione peroxidase and glutathione synthetase) more up-regulated in the NSPH groups with a concentration-dependent manner than the control one. Among A. veronii-infected fish, mortality rate was decreased with increasing NSPH replacement, where the NSPH40 group had the highest significant (p < 0.05) survival rate (83.33%). From overall results, NSPH can substitute 40% of the dietary FM protein in O. niloticus with promoting the fish’s immune competence, growth rate, digestive, and absorptive capability, and disease resistance.