Antioxidant peptides are commonly used as functional ingredient in the pharmaceutical industries. Here, we characterized the antioxidant peptides from mackerel muscle protein hydrolysates (MPHs). MPHs showing higher bioactivities were separated into seven groups by FPLC. MPH-3 which exhibited significantly higher (p < 0.05) DPPH scavenging activity (32.12 ± 3.01%) was fractionated using RP-HPLC to obtain purified fractions A and B, which were further subjected to MALDI-TOF/TOF-MS for mass fingerprinting. Fraction A exhibited the highest (p < 0.05) DPPH scavenging activity (34.11 ± 1.52%), and it contained 21 peptides characterized by LC-MS/MS-. Ten peptides were synthesized, and their antioxidant activities were evaluated; one of the peptides, ALSTWTLQLGSTSFSASPM, showed the highest (p < 0.05) DPPH scavenging activity (36.34 ± 4.64%) and another peptide, LGTLLFIAIPI, exhibited the highest (p < 0.05) SOD-like activity (28.94 ± 4.19%). The results of this study indicate that MPHs could serve as a suitable source of antioxidant peptides.