One of the most common approaches in bio-separation processes is the aqueous two-phase system (ATPS). To optimize these systems, thermodynamic modeling is used to obtain biomolecule-distribution between phases and also phase equilibria which are essential in the design of extraction units. Perturbation theory is used to describe fluid properties by means of intermolecular interactions. Statistical association fluid theory (SAFT) is the most popular perturbation theory-based model. Scientists then changed the reference fluid, resulting in the introduction of the successful PC-SAFT model. In this study, thermodynamic modeling for partitioning of Lysozyme, Bovine Serum Albumin (BSA) and Alpha-Amylase proteins in PEG/K2HPO4 ATPS have been studied. The restrictive primitive mean spherical approximation (RP-MSA) has been used for long-range interactions and PC-SAFT covers the short-range interactions. In fact, E-PCSAFT has been used instead of E-SAFT comparing to previous studies. The pure-component parameters of these systems are obtained using parameter fitting and compared to SAFT’s, thereby model parameters have been analyzed toward a better understanding of protein partitioning process.