The market share of eco-friendly vehicles to minimize global greenhouse gas (GHG) emissions is still lower than that of ICEVs, especially the diffusion of hydrogen fuel cell vehicle (HFCV) being at the market entry stage. At present, the penetration rate of HFCV is below the government target, it is necessary to examine the effectiveness of related government policies. To this end, this study identified the factors affecting consumers preferences and diffusion of HFCV in South Korea and based on consumer preferences and expectation levels for the vehicle attribute, the future market share by the fuel type of vehicle was forecasted. Concretely, this study analyzed the stated-preference data using a discrete choice model which reflects the consumer theory, and predicted the future diffusion trend of HFCV, by considering development in related technologies and changes in government policies. The results revealed that an improvement in consumers' uncertainties about hydrogen has a more important impact on the diffusion of HFCVs than the expansion of charging infrastructure. Further, to achieve the HFCV supply target set by the South Korean government, it is necessary to raise positive awareness of HFCV along with lowering purchase price for HFCV and improvement in related technology levels.