This study reviews the main problems of high air pollution levels at many urban cities and sustainability of the transportation fuels, and addressing their control measures using hydrogen energy system. In the world, majority of the transportation vehicle fleets consume the fuels derived from fossil resources. The development of economy activities indicate the increase in transportation services resulting in increased fuel consumption and high emissions, especially unregulated emission carbon dioxide, which is a greenhouse gas (GHG). Therefore, utilization of hydrogen as fuel in vehicle fleet would improve energy security and reduce the GHG emission. A feasibility of hydrogen energy system, which includes its resources, production technologies, storage, fuel transportation, dispensing and utilization, is analysed for the road transportation sector. In addition to this, the study highlights the technical issues and its control strategy for addressing the problems of the transportation system using the hydrogen. Moreover, hydrogen is the cleanest fuel, especially when coupled with renewable energy sources. The road transportation sector with hydrogen energy system would give the desirable results including high energy efficiency and zero carbon based emission (CO, CO2, HC, PM) resulting in strengthening of sustainability of the system. The Governments of many countries have made ambitious policies and provide strong financial support to research organizations including universities and institutions for development of hydrogen energy system. Many companies express strong interest in the commercialization of hydrogen fuelled vehicles either internal combustion engines based, fuel cell based or hybrid technology.