SummaryThe antioxidant activity and stability of endogenous peptides isolated from farmed hybrid catfish (Clarias macrocephalus × Clarias gariepinus) muscle (EPC) were characterised. EPC contained 69 peptides with 8–24 amino acid residues, varying hydrophobic amino acid (HBA) content and distinct sequences. Among the top five, peptides discovered in EPC were ARHSYGMLYCSCPPND, DTQAARKSDDDD, AEFPCGDRRC, AAVTEELFFAGL and LILQRRKFLRMKREKYGFIYKTHL. Histidine (16.33%) and tryptophan (15.66%) were the most common amino acids found in EPC. EPC demonstrated concentration‐dependent free radical (DPPH•/ABTS•+) and hydroxyl radical (OH•) scavenging activities, as well as metal chelating ability. The effect of pH, heating temperature and in vitro digestion on EPC's DPPH• scavenging activity was studied. Lowering the pH and increasing the heating temperature to 90 °C increased the DPPH• inhibitory activity. However, after in vitro digestion, around 44% of DPPH• inhibition was reduced. The findings confirmed that farm‐raised hybrid catfish muscle contained endogenous peptides with antioxidant properties.