We used a pulsed electric field (PEF) to treat four pentapeptides with similar amino acid sequences (KCHKP, KCHQP, QCHKP, and QCHQP). We then evaluated antioxidant activity of the pentapeptides according to ferric reducing antioxidant power (FRAP) and hydroxyl radical scavenging capacity. Structures of the peptides were determined by high performance liquid chromatography (HPLC), mid-infrared (MIR), circular dichroism (CD) spectroscopy, and nuclear magnetic resonance (NMR). The results indicated that antioxidant activities of KCHQP and QCHKP were increased by PEF, whereas those of KCHKP and QCHQP were reduced. The basic structures and functional groups of peptides were unaffected. PEF treatment reduced the alpha-helix contents of KCHQP and QCHKP, but increased those of KCHKP and QCHQP. Moreover, the chemical shifts at 14.46 ppm, 8.22 ppm, 7.87 ppm, 7.24 ppm, and 6.13 ppm attributable to hydrogen atoms of QCHKP shifted to the right, but the active hydrogens of QCHQP were not affected by PEF.