With the development of electromobility, car manufacturers have established and expanded the value chain for lithium-ion batteries. Specialised logistics for battery systems can help improve the environmental performance of the supply chain by increasing its efficiency and sustainability, taking into account the requirements for volumes and characteristics of battery systems and cell modules. One way to limit the carbon footprint is to shift the transport of battery products from road to rail. Focusing on the design of the transport system for battery systems and cell modules, our design starts with the special load carrier (SLC), as both goods are class nine dangerous goods according to the Agreement concerning the International Carriage of Dangerous Goods by Road (ADR). Based on the results of a functional analysis, the racks should be designed to fulfil the specific load carrier functions for cell modules and battery systems. The combination of SLC design and cargo space optimisation results in the best possible use of the volume and mass capacity of freight wagons for intercompany transport by rail. Special trailers are used for internal transport with electric trucks. All loading/unloading, handling, storage and transport processes are fully automated to ensure efficient internal material flow. An application example shows that around 14,300 tonnes of CO2e can be saved per year for the supply chain of cell modules and battery systems by rail. This result points the way to further practices and improvements in the sustainability of automotive or other supply chains.