Protein release from poly(D,L-lactide-co-glycolide) (PLGA) microspheres in an aqueous environment is governed by the diffusion of the protein through an autocatalytically degrading polymeric matrix. Many attempts have been made to model the release rate of proteins from biodegrading matrices, but the transport parameters involved in the process are not fully established at the microscale level. The aim of this work was to develop a new mathematical model taking into account the temporal evolution of the radial protein distribution during release, and to provide physical insight into the relation between local transport features and microsphere degradation. The model was validated by comparing its predictions with the experimentally determined protein concentration profiles in PLGA microspheres loaded with tetramethylrhodamine-labelled bovine serum albumin (BSA-Rhod) as a model protein. Morphological studies were carried out by scanning electron microscopy (SEM), while release kinetics and time-dependent BSA-Rhod concentration profiles within the microspheres were studied by a confocal laser scanning microscopy (CLSM)-assisted technique. The model, based on a modification of Fick's second law of diffusion, could closely fit the experimental protein radial distribution profiles in the microspheres as a function of time. It is also a useful tool to ab initio design protein release devices using degrading matrices.