The present study examined the impacts of varying amounts of selenium nanoparticles (Se-NPs) as a natural antioxidant and metabolic regulator on growth performance, antioxidant capacity, digestive enzymes and immune resistance of Oreochromis niloticus challenged to Aspergillus flavus infection. For 60 days, fish were fed the experimental diet of 30% crude protein up to apparent satiation three times a day. Se-NPs were added to the control diet at different levels of 0.0 (control), 0.5 (T1), 1.0 (T2) and 1.5 (T3) mg/kg diet to fed monosex Nile tilapia fingerlings with average initial weight (4.5 ± 0.5 g). Fish were randomly distributed in 12 tanks 100 L at a density of 20 fish per tank after 2-week acclimation to represent four treatments in triplicates. The results indicated that the growth indices, feed efficiency and survival rate were significantly enhanced (P < 0.05) by incorporating Se-NPs up to 1 mg/kg diet. Furthermore, the haemato-biochemical parameters, digestive enzymes activity and antioxidant capacity of the fish were significantly improved (P < 0.05) at T2. When the fish were challenged with Aspergillus flavus, a decreasing mortality rate was observed, which clearly shows that selenium nanoparticles boosted the fish’s immune response at T2. The intestinal morphology as villus length, villus width, muscular fibres layer thickness and absorption intestinal zone after challenged with A. flavus infection were considerably enhanced (P < 0.05) by incorporating all Se-NP levels. Histopathological score significantly improved (P < 0.05) for the hepatopancreatic, intestinal, gills and muscle tissues at T2. The present study concludes that selenium nanoparticles up to 1.0 mg/kg diet can be efficiently used in tilapia feed to help boost fish production, immune system response and histopathological parameters.