Several countries have revised their targets in recent years to reach net-zero CO₂ emissions across all sectors by 2050, and the transport sector is responsible for a significant share of these emissions. This study compares possible pathways to decarbonise the transport sector including passenger cars, light commercial vehicles and heavy commercial vehicles. To do so, we explore 125 scenarios by varying the share of battery and hydrogen-based fuel cell electric vehicles in each of the three categories above independently. We further model the decarbonisation of the industrial hydrogen demand using electrolysers with hydrogen storage. To explore the potential role of electric and hydrogen transport, as well as their trade-offs, we use GRIMSEL, an open-source sector coupling energy system model of Switzerland which includes the residential, commercial, industrial and transport sectors with four energy carriers, namely electricity, heat, hot water and hydrogen. The total costs are minimised from a social planner perspective. We find that the decarbonisation of the transport sector could lead, on average, to a 12% increase in costs by 2050 and 1.3 MtCO₂/year which represents a 90% CO₂ emissions reduction for the whole sector, compared to fossil-based transport. Second, the transport energy self-sufficiency (i.e. the share of domestic electricity generation in final transport demand) may reach up to 50% for the scenarios with the largest share of battery electric vehicles, mainly due to a smaller energy demand than with hydrogen vehicles. Third, more than three quarters of the industrial hydrogen production is met by local photovoltaic electricity coupled with battery at minimum costs, i.e. green hydrogen. Finally, the use of hydrogen as an energy carrier to store electricity over a long period is not cost-optimal.