This study aimed to obtain antioxidant peptides from perilla seed meal (PSM), which is normally discarded as an industrial waste during seed oil extraction. PSM protein was hydrolyzed using trypsin and fractionated by ultrafiltration. Molecular weight fraction (<3 kDa) with the highest antioxidant activity was purified using prep‐HPLC and analytical HPLC. The purification fold of the peptide (fraction V) obtained from PSM protein hydrolysate on DPPH radical scavenging activity, ABTS radical scavenging activity, and reducing power was 1.79‐, 1.59‐, and 1.81‐fold, respectively, after the three‐step purification procedure. The sequence of the purified peptide from fraction V that exhibited free radical scavenging activity and reducing power was identified as Ile‐Ser‐Pro‐Arg‐Ile‐Leu‐Ser‐Tyr‐Asn‐Leu‐Arg (1,330.77 Da). These results demonstrate that PSM protein, a by‐product from the oil seed extraction, can be used as a source of natural antioxidant peptides for food and/or nutraceutical applications.