This paper presents a simulation-based analysis of hybrid and plug-in hybrid propulsion system concepts for diesel-electric multiple unit regional railway vehicles. These alternative concepts primarily aim to remove emissions in terminal stops with longer stabling periods, with additional benefits reflected in the reduction of overall fuel consumption, produced emissions, and monetary costs. The alternative systems behavior is modeled using a backward-looking quasi-static simulation approach, with the implemented energy management strategy based on a finite state machine control. A comparative assessment of alternative propulsion systems is carried out in a case study of a selected regional railway line operated by Arriva, the largest regional railway undertaking in the Netherlands. The conversion of a standard diesel-electric multiple unit vehicle, currently operating on the network, demonstrated a potential GHG reduction of 9.43–56.92% and an energy cost reduction of 9.69–55.46%, depending on the type of service (express or stopping), energy storage technology selection (lithium-ion battery or double-layer capacitor), electricity production (green or grey electricity), and charging facilities configuration (charging in terminal stations with or without additional charging possibility during short intermediate stops) used. As part of a bigger project aiming to identify optimal transitional solutions towards emissions-free trains, the outcomes of this study will help in the future fleet planning.