The paper is focused on an example of a solution for the sustainability of transport and mobility with the application of discrete computer simulation. The obtained results from the realized simulation were complemented with the selected multi-criteria decision-making method, namely the analytic hierarchy process (AHP) method. The paper describes the use of the simulation model for obtaining characteristics of alternative solutions that were designed for the needs of transport sustainability. The aim is to address the problem of traffic congestion in urban agglomerations. The simulation model serves as a means to provide information for the needs of their analysis by multi-criteria evaluation by the AHP. The methodology is based on a combination of computer simulation and multi-criteria decision-making and presents a useful tool that can be used in the field of transport sustainability. The paper notes methods to implement analysis of alternative solutions in transport. However, this procedure can also be used to solve other problems in the field of logistics systems. The paper compares five possible solutions for the organization of transport at intersections. Multi-criteria decision-making was realized based on 12 criteria. The result was the solution that reduced the length of congestion in almost all directions, with a maximum shortening of 69 m and a shortening of the average delay by 26 s compared to the current state.