A successful decarbonisation of the European Union, coupled with a high integration of renewable energy and ambitious targets for energy efficiency, can only be reached with a significant contribution from the transportation sector. It currently represents a quarter of the total greenhouse gas emissions and is shifting from fossil fuels to alternative energy carriers (biofuels, e-hydrogen, electricity) and propulsion systems (hybrid, electric and fuel-cell vehicles). Decarbonising this sector can follow multiple pathways, each having different costs, impacts and implications for the other sectors (industry, residential and services). This paper presents a method to analyse the impact of each decarbonisation pathway in the mobility sector on the overall energy system, using the EnergyScope model. The proposed methods include: (i) an estimation of the hourly demand profiles for short- (local) and long-distance mobility, using annual projections and traffic measurements; (ii) the development of black-box vehicle models of road, rail and aviation technologies; (iii) the modelling of the associated infrastructures, from the fuel conversion processes to the charging stations; and (iv) the use of Monte-Carlo-based tools to account for technical and economic uncertainties. This method allows to assess the effects of mobility decarbonisation pathways on the energy system, from the large-scale deployment of vehicle-to-grid technologies to the integration of biofuel- and hydrogen-based vehicles. France has been taken as case study, considering 2050 as time horizon. The results showed the importance of a holistic approach to suggest cost- and energy-efficient decarbonisation pathways in the transport sector that can affect the overall energy system.