This article addresses certain issues related to the application of various cargo delivery systems that facilitate energy transition in cities and agglomerations. The main purpose of this article was to estimate the effects resulting from the application of a cargo delivery system that is an alternative to road transport within the area of the Szczecin agglomeration. The study applied the following research methods: literature review, mathematical computations, case study, and observation. The article estimated the volume of transport external costs’ reduction resulting from shifting cargo deliveries from road to rail transport in said agglomeration, applying the EU methodology to specify the amounts of external costs generated by individual modes and means of transport. The completed studies have demonstrated that the application of a rail-based cargo delivery system in the Szczecin agglomeration would enable a considerable reduction in the external costs generated by transport, thus supporting energy transition in said area. The findings also make it possible to conclude that the proposed solution may bring some other effects, such as a reduction in the number of diesel-powered heavy goods vehicles, reduced road congestion, and the increased safety of residents, as well as supporting electromobility and low-emission mobility policies in cities and agglomerations.