Aqueous two-phase extraction (ATPE) is a liquid-liquid extraction (LLE) technique which is viable as a continuous protein purification unit operation for the manufacture of therapeutic proteins. A shift from batch to continuous manufacturing in this industry has been encouraged by regulatory bodies, including the Food and Drug Administration (FDA), as it is expected to increase the quality and consistency of the product and decrease manufacturing costs. For ATPE to compete with current batch protein purification procedures, a multi-stage operation can be used to achieve a high purity and yield. However, there is a lack of reliable modelling techniques in the design of multi-stage ATPE; as a result, its design and operation is often reliant on both individual expertise and trial and error. To reduce this, there is a need to develop modelling techniques to aid in system design. In this study we present a modified equilibrium binary separation method to predict an optimal number of stages in a multi-stage system. The model is validated against data, for both traditional LLE and ATPE, in a counter-current multi-stage operation [Rosa et al., 2009a, Warade et al., 2011]. The model is then applied to a case study separation of phycocyanin from lysozyme using PEG-phosphate ATPE. The model is successfully used to predict a suitable design of a counter-current multistage system to optimise purity and yield of the target protein. The approach provides the basis with which to design general ATPE-based continuous downstream processes incorporating extraction, back-extraction and washing steps.