We present a detailed study of the diffusive transport of proteins across a fluid phase boundary within aqueous two-phase systems. The aim of the work is to investigate whether local effects at the phase boundary cause a retardation of the diffusive transport between the phases. Possible modifications of interfacial mass transfer could be due to protein adsorption at the phase boundary or local electric fields from electric double layers. Experiments with a microfluidic system have been performed in which protein diffusion (bovine serum albumin and ovalbumin) within a bilaminated configuration of two phases containing polyethylene glycol and dextran is analyzed. A one-dimensional model incorporating phase-specific diffusion constants and the difference in chemical potential between the phases has been formulated. A comparison of experimental and simulation data shows a good overall agreement and suggests that a potential local influence of the phase boundary on protein transport is insignificant for the systems under investigation.