The most important features of the drone (unmanned aerial vehicle) are its survivability, noise immunity and secrecy. In this context, the threats that arise during the protection of weapons depots and important public facilities have been analyzed. The parameters of the early detection of drone attacks have been studied. The possibilities of countering the unmanned aircraft attack by means of air defense and electronic warfare systems are considered. In the geographic information system for an electronic map of the area, a simulation model is proposed. The model has an aircraft route organizer that allows analyzing possible flight directions at given altitudes and speeds on various route segments. With fixed initial conditions and repeated model execution, a statistically significant result can be obtained in the form of a mathematical probability of defeat (neutralization) of an unmanned aerial vehicle. This feature is implemented using the definition in the model of the states and events of an unmanned aerial vehicle along segments of the route. For example, a case when the device enters the zone of action of one or more air defense means. Or, an example of another situation, when the drone with a certain probability is affected by air defense units. In the model it is possible to calculate and correct the probabilities of detection, neutralization and hitting of the drones. If in the process of the simulation model re-running, negative results in covering the objects are obtained, then the locations of observation points, electronic warfare and anti-aircraft defense facilities should be changed. The newly formed detection, cover and defeat zones should ensure the neutralization of the UAV in a potentially dangerous direction. In addition, on the base of results of the model, this approach can be used for the protection of other electronic warfare and air defense systems with higher likelihood of destruction and neutralization of the drones.