Ferimzone Z is a fungicide for effectively controlling rice blast. Under light irradiation conditions, it undergoes a rapid conversion to its E-stereoisomer. Given the importance of isomers in risk assessments of residues in crops, an analytical method was developed for individual isomer quantification. A comparative analysis performed using two columns in HPLC-MS/MS demonstrated that the isomers were successfully separated using the Cadenza column. For the brown rice sample preparation, 5 g of the homogenized sample was saturated with 7 mL of water. The sample was then extracted with a 10 mL mixed solvent of acetonitrile and ethyl acetate (1:1, v/v) that contained 0.1% formic acid, and it was subsequently partitioned with magnesium sulfate and sodium chloride. The upper layer was purified using dSPE containing C18 and PSA sorbents. The established method was subjected to method validation, and it showed recovery rates of 90.6-98.8% (RSD ≤ 3.9%) at concentrations of 0.01, 0.1, 2 mg/kg, with a soft matrix effect (%ME) ranging from -3.1% to +6.5%. This method can be employed in monitoring studies of brown rice to determine the conversion ratio from the Z isomers to the E isomers.