A method has been developed for the separation of two geometrical isomers of the {Fe[3-(2-pyridyl)-5,6-diphenyl-1,2,4-triazine]3}2+([Fe(PDT)3]2+) using ion-pair reversed-phase high performance liquid chromatography (RP-HPLC). The effects of the chromatographic conditions, such as the content of acetonitrile and the type and concentration of the ion-pair reagents (sodium perchlorate (NaClO4) or sodium dodecyl sulfate (SDS)) in the binary mobile phase (acetonitrile and water), on the retention factor (k), resolution, and selectivity were iscussed. It was found that no matter how the ion-pair reagent was NaClO4 or SDS at different concentrations, the acetonitrile content in the mobile phase has good linear regression equations with the ln k of the two isomers. It was also observed that SDS showed more positive effect on the k of the two geometrical isomers than that of NaClO4. Moreover, the separation of the two isomers in the ternary mobile phase (acetonitrile, methanol and water) was developed. The chromatographic conditions, including the content of the organic modifier (acetonitrile and methanol) and the type and concentration of the ion-pair reagents (SDS and NaClO4), were optimized. Two geometrical isomers were rapidly and successfully separated under the optimized conditions, which used acetonitrile/methanol/water (20: 50: 30, v/v/v) as the mobile phase and 60 mmol/L NaClO4 as the ion-pair reagent. Good linear regression equations between the peak areas and concentrations for the two isomers were obtained. The detection limits of the fac-isomer and mer-isomer were 4.28 and 3.44 ng/mL (S/N = 3), respectively.