Protein adsorption onto foreign material is the beginning of a biological process that results in induced thrombosis that leads to a response that may be detrimental to the body. The prevention of blood plasma protein adsorption is a major factor in promoting biocompatibility of biomaterials with blood plasma. The application of coating biomaterial surfaces with poly(ethylene oxide) (PEO) has been very popular in biocompatibility studies. Theoretical studies have created models that have based protein adsorption on surfaces coated with polymers on free energies (van der Waals, hydrophobic interactions, and steric repulsions). The random sequential adsorption (RSA) model is a theoretical model that postulates that randomly distributed polymers and their obstruction of adsorption sites is a major factor that affects the random placement of protein adsorption based on the availability of the remaining unobstructed adsorption sites. This work examines the simulation of how the arrangement of polymer layers prepared by self-assembled monolayers (SAM) and physical adsorption affects the diffusion of the arrangement of proteins on the surface based on the RSA model. The model in this work extends the RSA model by considering the exact arrangement of polymers on the surface as well as dynamic rearrangements of adsorbed proteins that lead to a more closely packed layer. The modified RSA models are compared to previously reported experimental protein adsorption on PEO grafted surfaces using SAMs as well as physically adsorbed copolymers of PEO. Our results show that accounting for underlying polymer arrangement and protein rearrangements post-adsorption significantly improves the predictions of the RSA model. The simulations are compared with experimental observations for the polymers: EG1OH, EG2OH, EG4OH, EG6OH, EG17OCH3, EG23OH, EG46OH, and EG115OH. The effect of polymer grafting density and polymer chain length of PEO on protein adsorption are also investigated. These results provide a more robust model for predicting protein surface adsorption on hydrophilic polymer coated surfaces as a function of the polymer chain length, grafting density, protein size, protein surface sub-diffusion, and polymer layer structure. This paves a path for the design of high performance anti-fouling surface coatings.