Fuzzy cognitive maps (FCM) have been broadly employed to analyze complex and decidedly uncertain systems in modeling, forecasting, decision making, etc. Road traffic flow is also notoriously known as a highly uncertain nonlinear and complex system. Even though applications of FCM in risk analysis have been presented in various engineering fields, this research aims at modeling road traffic flow based on macroscopic characteristics through FCM. Therefore, a simulation of variables involved with road traffic flow carried out through FCM reasoning on historical data collected from the e-toll dataset of Hungarian networks of freeways. The proposed FCM model is developed based on 58 selected freeway segments as the “concepts” of the FCM; moreover, a new inference rule for employing in FCM reasoning process along with its algorithms have been presented. The results illustrate FCM representation and computation of the real segments with their main road traffic-related characteristics that have reached an equilibrium point. Furthermore, a simulation of the road traffic flow by performing the analysis of customized scenarios is presented, through which macroscopic modeling objectives such as predicting future road traffic flow state, route guidance in various scenarios, freeway geometric characteristics indication, and effectual mobility can be evaluated.