The railway is one of the most energy-efficient modes of transport, helping to enhance the environment and public health in cities and agglomerations. In this paper, the authors raise the issue of the construction of an underground railway route in Wrocław (Poland) to allow the organization of the suburban rail system in the agglomeration. There are many concepts for the construction of this route, but so far none has been realized. Therefore, it is important to design the route properly. Here, five options for this tunnel are considered and evaluated. To make such an evaluation, the authors construct a modified ant colony optimization algorithm (ACO). The “classic” algorithm considers the determination of the shortest route. The modification of the algorithm will allow a more accurate analysis of the issue, taking into account more parameters than just the length of the route. These are the location of traffic generators in the city center, the number of inhabitants neighboring the stations, and the number of tram or bus lines integrated with the railway. The presented method and exemplary case study should allow for the evaluation, introduction, or development of the city railway.