Cholesterol ester hydroperoxide (CEOOH) is one of the main lipid oxidation products contained in oxidized low-density lipoprotein (LDL). Previous studies suggest that CEOOH in oxidized LDL is closely related to several diseases. Of the oxidation mechanisms of cholesterol ester (CE) in vivo, it has been suggested that enzymatic oxidation induced by lipoxygenase (LOX) plays an important role. Thus, we attempted to develop a method that can evaluate the enzymatic oxidation of CE via the diastereoselective separation of CEOOH bearing 13RS-9Z,11E-hydroperoxy-octadecadienoic acid (13(RS)-HPODE CE). Firstly, we synthesized the standard of 13(RS)-HPODE CE. Using this standard, the screening of analytical conditions (i.e., column, mobile phase, and column temperature) was conducted, and separation of the diastereomers of 13(RS)-HPODE CE was achieved. The diastereoselective separation of 13(RS)-HPODE CE was also confirmed by LC-MS/MS. The developed method (column, CHIRALPAK IB N-3; mobile phase, hexane:ethanol (100:1, v/v); column temperature, 0 °C) can distinguish between enzymatic oxidation and other oxidation mechanisms of CE. Thus, the method can be expected to provide a greater understanding of the biochemical oxidation mechanisms in vivo. Such information will be essential to further elucidate the involvement of CEOOH in various diseases.