Protein derived from purple wheat bran was hydrolyzed sequentially using alcalase proteases for the production of antioxidant peptides. Purple wheat bran protein (PWBP) hydrolysates were fractionated using size-exclusion (G-25) and ion-exchange chromatography methods to identify the structure of antioxidant peptides. The free radical scavenging activity of peptides purified from PWBP hydrolysates was evaluated using superoxide anion radical-scavenging activity and determination assays of Trolox equivalent antioxidant capacity (TEAC). Results demonstrated that purple wheat bran peptide F4-4 exhibited the highest antioxidant activity among other hydrolysates. F4-4 was further identified as Cys-Gly-Phe-Pro-Gly-His-Cys, Gln-Ala-Cys, Arg-Asn-Phe, Ser-Ser-Cys, and Trp-Phe by high performance liquid chromatography (HPLC) spectrometer coupled with Orbitrap Elite™ mass spectrometer (LC-MS/MS). Antioxidant peptides 2 and 4 showed improved stability when the temperature was lower than 80 °C. These peptides also demonstrated good digestive stability in vitro system by simulating gastrointestinal digestion.