The paper presents a mathematical model of functioning of the system of information protection (IPS) from unauthorized access (UA) in automated systems (AS). This model was developed in framework of the CPN Tools software environment. For convenience, visibility and preservation of logical integrity, the model is divided into subsystems using the tools built into CPN Tools. The model is necessary for a computational experiment, namely, to study the real consumer properties of IPS from UA in AS, as well as for development a software package for analyzing and quantifying the effectiveness of these systems. The results of the simulation of functioning of the IPS from the UA in the AS can be presented in the form of various characteristics of each state, which characterize the work of the system as a whole and its subsystems. The developed simulation model can be used to create similar systems, during their operation, during certification of information security systems, during certification of informatization facilities, and during periodic monitoring of used information protection software at these facilities. The programming language Meta language used by CPN Tools allows you to monitor random transitions of the marker from the initial state to the final through the intermediate one, to set time delays, etc. The simulation model of IPS from UA to AS will be used in further studies to build the models of impact of various types of threats to this system according to the bank data threats to information security of the Federal Service for Technical and Export Control of Russia.