Hydrogen, as a clean and versatile energy carrier, holds immense promise for addressing the world’s growing energy and environmental challenges. However, hydrogen-based energy systems face challenges related to efficient storage methods, energy-intensive production, refueling processes, and overall cost-effectiveness. To solve this problem, a superstructure was developed that integrates overall technologies related to hydrogen energy transportation. This study synthesizes process pathways for hydrogen energy transportation method including energy carrier production, storage, and refueling, based on the developed superstructure. The techno-economic analysis was conducted to evaluate the performance of each transportation pathway and compare it with conventional fossil fuel transportation system. Process performance criteria, including unit production cost (UPC), energy efficiency (EEF), and net CO2 equivalent emissions (NCE), serve as indicators for process performance. By comparing technological pathways, we can propose the most economically and environmentally optimal energy refueling route. Additionally, sensitivity analyses were performed on various external factors, identifying influential variables in the decision-making process for hydrogen production, storage, and refueling strategies, while also elucidating technological limitations.