Edible bird's nest (EBN) is widely consumed as a delicacy and traditional medicine amongst the Chinese. In the present study, for the first time, the antioxidant properties of an EBN pepsin-trypsin hydrolysate of the swiftlet species Aerodramus fuciphagus and its ultrafiltration fractions were investigated. Thirteen peptides with molecular weights between 514.29 and 954.52 Da were identified in the EBN fraction with the use of mass spectrometry. Two novel pentapeptides Pro-Phe-His-Pro-Tyr and Leu-Leu-Gly-Asp-Pro, corresponding to f134-138 and f164-168 of cytochrome b of A. fuciphagus, indicated the highest ORAC values of 14.95 and 14.32 μM of TE μM-1 peptide, respectively. Both purified peptides showed resistance against simulated gastrointestinal proteases. In addition, both peptides had no in vitro cytotoxicity on human lung MRC-5 cells and prevented human liver carcinoma HepG2 cellular damage caused by hydroxyl radicals. Therefore, it is suggested that EBN protein hydrolysates are a good source of natural antioxidants and could be applied as nutraceutical compounds.