A feeding trial was conducted to evaluate the effect of dietary protein hydrolysates from common carp (Cyprinus carpio) by-products on the antioxidant status of zebrafish (Danio rerio). Common carp by-product was hydrolysed using Alcalase to a degree of hydrolysis of 15%. The zebrafish were fed for 44 days with four different diets with increasing levels of carp by-product hydrolysates (CBH0: 0 g/kg; CBH25: 25 g/kg; CBH50: 50 g/kg; CBH100: 100 g/kg). The gills, muscle and brain were dissected at the end of the feeding trial in order to evaluate the total antioxidant capacity against peroxyl radicals (ACAP) and lipid peroxidation (TBARS). Although total antioxidant capacity did not show differences in muscle (p > 0.05), lipid peroxidation was reduced in the muscle of fish fed the CBH50 diet. Brain lipid peroxidation showed a significant reduction (p < 0.05) in all groups when compared with the control diet CBH0. Antioxidant properties of protein hydrolysates indicate their potential as nutraceuticals since (a) a reduction in muscle lipid peroxidation was verified, implying that their use could enhance the quality and shelf life of fish fillets; and (b) a decrease in brain lipid peroxidation was registered, highlighting the potential use of fish protein hydrolysates for the prevention of neurodegenerative diseases.