In this study, we report the separation of Pd(II) and Rh(III) in a chloride solution using a polymer inclusion membrane (PIM). We designed a trioctyl(dodecyl) phosphonium chloride (P88812Cl) ionic liquid as a metal carrier for the PIM separation system. The effects of PIM composition and experimental conditions were systematically investigated. The concentrations of hydrochloric acid in the feed solution and thiourea in the receiving solution were found to play a crucial role in the success of selective separation. Under the optimized conditions, Pd(II) could be effectively separated from Rh(III) with a 98% recovery yield and 99% purity. We also compared the performance of our designed carrier, P88812Cl, to that of commercially available ionic liquid trihexyl(tetradecyl) phosphonium chloride (P66614Cl) using a 7-cycle reusability test. The P88812Cl showed a more stable performance and better durability compared with those of the commercial ionic liquid carrier.