Synaptic transmission is the main process providing cross-connecting activity among neurons in the central nervous system (CNS). It is commonly accepted that a synaptic contact consists of the complex of pre- and post-synaptic membranes contacting with astrocytes. The transmission is accomplished through several steps. Initially, neuromediators stored in pre-synaptic vesicles release into a synaptic cleft. Then they diffuse to post-synaptic membrane where neuromediators bind to specific receptors cause their activation. Finally, in the most cases except acetylcholine the mediators will be removed from the cleft either by convectional diffusion or by re-uptake. There is much experimental evidence indicating a structural ordering of both vesicles with pre-synaptic contacts and receptor localization. In particular, the number and eventual position of glycine receptors (GlyRs) on a post-synaptic membrane are defined by the structural data of the GlyR-gephyrin complex. In this case the membrane cluster of GlyR can have central, divided and rear localizations. In the present study, the 3D mathematical model of a neuronal bouton with a cluster localization of glycine receptors (GlyRs) on the post-synaptic membrane was developed. GlyR provides a transmembrane current of Cl- mediating a hyperpolarization of neuronal membranes. The forming of inhibitory postsynaptic potential (IPSP) and an electro-diffusion of chloride ions were evaluated by applying the boundary problems for a Poisson’s equation and a non-steady-state diffusion equation, respectively. The local changes ion concentration near the post-synaptic membrane, mediated by GlyRs activation, can raise up to 80–110% from the initial level. It is remarkable that the central spatial localization of GlyRs in the cluster had a considerable difference both in the chloride ion concentration changes (6%) and IPSP (17%) compared to the divided or rear localization. Thus, a spatial polymorphism of the post-synaptic density of GlyRs is important to form a physiological response to a neuromediator release.