In this study, a sulfoxide residue bonded silica stationary phase was prepared for the separation of polychlorinated biphenyls (PCBs) from mineral oils, and its properties were investigated. Organic sulfide was attached to a silica surface by an amide bond, and the bonded sulfide residues were oxidized to sulfoxide with hydrogen peroxide to afford sulfoxide and sulfone residues bonded to the stationary phases (0.84 and 0.63 mmol of sulfur bonded per gram, respectively). The oxidation states of sulfur atoms bonded on the stationary phases could be determined using high-resolution X-ray fluorescence spectra. The modified stationary phases, especially sulfoxide-bonded one, separated PCBs from mineral oils (paraffin-based transformer oils) more efficiently than aminopropyl silica or other polar stationary phases that have been used for the cleanup of PCBs. The chromatographic parameters for an aliphatic hydrocarbon (eicosane) and some PCB congeners indicated strong retention of highly chlorinated biphenyls by the sulfoxide-bonded silica compared with the aminopropyl silica. A cleanup procedure was established for simple determination of PCBs in mineral oil samples using the sulfoxide-bonded silica packed column fractionation. The analytical method was validated using a certified reference material and a PCB-fortified transformer oil sample.