The focus on pathways to reduce the use of fossil fuels in the transport sector is intense in many countries worldwide. Considering that biofuels have a limited technical production potential and that battery electric vehicles suffer from technical limitations that put constraints on their general use in the transport sector, hydrogen-fuelled fuel cell vehicles may become a feasible alternative. Introduction of hydrogen in the transport sector will also transform the energy sector and create new interactions. The aim of this paper is to analyse the consequences and feasibility of such an integration in Sweden. Different pathways for hydrogen, electricity and methane to the transport sector are compared with regard to system energy efficiency. The efficiencies for hydrogen and electricity are used for estimating the energy resources needed for hydrogen production and electric vehicles for a future Swedish transport sector based on renewable fuels. The analysis reveal that the well to wheel system efficiencies for hydrogen fuel cell vehicles are comparable to those of methane gas vehicles, even when methane gas is the primary energy source. The results further indicate that an increased hydrogen demand may have a less than expected impact on the primary energy supply in Sweden.