Owing to the recent increase in the global demand for Co, new cobalt–nickel refinery capacity is required. While solvent extraction is one of the most important separation and purification techniques in hydrometallurgy, pertraction, also called membrane-based solvent extraction, offers various advantages over conventional solvent extraction. In this study, pertraction was used to purify a pregnant leach solution obtained from spent hydrotreatment catalysts that had been produced by Minemet. A block flow diagram and mass balance for the cobalt–nickel refinery were developed and used in the experimental design. Extraction isotherms were determined as well as mass transfers optimised using a circulating batch pertraction setup for both synthetic and industrial cobalt–nickel mixed metal solutions. A comprehensive set of models was applied to translate the experimental data into a conceptual design of the industrial cobalt–nickel pertraction refinery to process pregnant leach solution from the Minemet plant.