As a countermeasure to the greenhouse gas problem, the world is focusing on alternative fuel vehicles (AFVs). The most prominent alternatives are battery electric vehicles (BEV) and fuel cell electric vehicles (FCEVs). This study examines FCEVs, especially considering hydrogen refueling stations to fill the gap in the research. Many studies suggest the important impact that infrastructure has on the diffusion of AFVs, but they do not provide quantitative preferences for the design of hydrogen refueling stations. This study analyzes and presents a consumer preference structure for hydrogen refueling stations, considering the production method, distance, probability of failure to refuel, number of dispensers, and fuel costs as core attributes. For the analysis, stated preference data are applied to choice experiments, and mixed logit is used for the estimation. Results indicate that the supply stability of hydrogen refueling stations is the second most important attribute following fuel price. Consumers are willing to pay more for green hydrogen compared to gray hydrogen, which is hydrogen produced by fossil fuels. Driver fuel type and perception of hydrogen energy influence structure preference. Our results suggest a specific design for hydrogen refueling stations based on the characteristics of user groups.