Exopolysaccharide (EPS)-producing bacteria were isolated from the intestines of freshwater fish as prebiotics. Among the isolates, Bacillus sp. P1 was the potent EPS producer, with a high EPS production, and was then identified as Bacillus subtilis P1 based on 16S rRNA and biochemical characteristics. The produced microbial EPS was characterized by its functional groups by FTIR, showing a 90.20% correlation to inulin, while the EPS molecular weight was approximately 105 Da with a high PDI (>1.5). Moreover, the EPS from B. subtilis P1 was assessed for prebiotic properties by growing probiotic bacteria, and significant cell growth occurred in sugar-free TSB with 0.5% EPS (p < 0.05). EPS exhibited approximately 55.37% DPPH radical scavenging at 20 mg/mL and inhibited certain fish pathogens at 400 μg/mL (10–13 mm inhibition zone). Low EPS cytotoxicity was confirmed (<1% hemolysis) prior to use as immunobiotics in Nile Tilapia (Oreochromis niloticus) diet supplementation. Nile tilapia growth and immune response were monitored after feeding with control (C), basal diet (BD), and treatment (T): BD + EPS 5 g/kg. In the T-group, the weight gain (WG), % specific growth rate (SGR), and average daily gain (ADG) significantly increased compared to the control (p < 0.05) by week 4, with no negative effects on blood chemistry parameters. Lysozyme activity and respiratory burst activity in T-groups were significantly higher than the control (p < 0.05), with a 50% RLP survival rate of Nile Tilapia infected by Aeromonas veronii in the T-group after a two-week challenge. On the other hand, the proximate analysis revealed higher protein content in the T-group. These findings suggest that EPS from B. subtilis P1 in fish diets efficiently supports fish growth and stimulates innate immune response in Nile Tilapia, thus showing potential as the immunobiotics for aquaculture.