This study aims to design energy supply systems from various energy sources for transportation sectors and comparatively analyze the life cycle cost of different scenario-based systems. For components of the proposed energy supply system, we consider a typical oil refinery, byproduct hydrogen system, renewable energy source (RES)-based electric generation system and existing electricity grid. We also include three types of vehicles in transportation sector such as internal combustion engine vehicle (ICEV), electric vehicle (EV), fuel cell vehicle (FCV). We then develop various energy supply scenarios which consist of such components and evaluate the economic performance of different systems from the viewpoint of life cycle cost. Finally we illustrate the applicability of the proposed framework by conducting the design problem of energy supply systems of Jeju, Korea. As the results of life cycle cost analysis, EV fueled by electricity from grid is the most economically feasible. In addition, we identify key parameters to contribute the total life cycle cost such as fuel cost, vehicle cost, infra cost and maintenance cost using sensitivity analysis.