Raw milk cheeses have unique flavor and texture characteristics not obtainable in cheeses made from pasteurized milk. However, cheeses made from pasteurized milk are widespread, primarily for public health reasons. Pulsed electric field (PEF) treatment as a non-thermal pasteurization method has shown its ability to keep the flavor and natural characteristics of food samples intact, thus providing advantage over conventional heat processing. In this study, PEF treatment was performed in a continuous treatment chamber, consisting of two parallel stainless steel electrodes separated by a 50-mm-thick insulator. A 30-kV pulse generator was used to deliver bi-polar square waveform electric field to milk sample. Pulse width was 2 µs; pulse frequency was 2 Hz, and up to 120 pulses were applied. Cheese curds were made from raw milk, pasteurized milk, and PEF-treated milk, and their proteolysis processes were compared using curd slurry incubated at 30 °C for 5 days. The profiles of water-soluble peptides were measured using an reversed-phase high-performance liquid chromatography (RP-HPLC) system. The concentration of free amino acids was measured by Cd–ninhydrin method. Results indicated that PEF-treated milk has intermediate proteolysis profiles between raw milk and pasteurized milk in terms of peptide and free amino acid concentration. The results showed the potential of making high-quality cheeses by PEF treatment without sacrificing the natural characteristics of the cheeses.