COP21 resulted in a major global agreement to reduce greenhouse gas emission to limit the Earth’s rising temperature to <2°C. Transport has a key role in the transition to a clean low carbon energy system. The aim of this work was to develop optimum scenarios for the implementation of alternative low carbon road transport fuels to replace conventional fuels of gasoline and diesel using the systems analysis model MESSAGE. The results show that technological breakthroughs to enhance efficiency and cost reduction of solar fuels will enable them to compete with gasoline and diesel in meeting the demand for road transport fuels. It also found that that production of synthetic fuels can significantly contribute to reducing consumption of crude oil while reducing CO2 emission by 80 per cent by 2050. Compared with previous literature, our work considers synfuels from fossil fuels can compete with biomass‐derived fuels, and it shows potential transition scenarios in the road transport sector to replace gasoline and diesel in fossil fuel‐dependent economies considering Saudi Arabia as a case study. Solar fuels appear as the most promising for reducing emission, albeit at a high price. Carbon abatement costs are found to range between $121 and $517/Ton, between 2015 and 2050. Feasible implementation of solar and synthetic fuels was also found to depend on the targeted CO2 emission, fuel efficacy, penetration of public transport and economic growth.