A future energy system for road transport requires optimised energy use and primary energy decarbonisation to achieve global CO2 reduction goals. Simultaneously decarbonising transport with other sectors of the economy places additional demands on limited low-carbon energy sources, requiring efficient processes within a fuel pathway from energy source to energy use. Battery electric vehicles (BEVs) and fuel-cell electric vehicles (FCEVs) are low-carbon options that reduce tailpipe emissions, but differ in overall efficiency, associated carbon intensity, and cost. Current commercialised technologies, as well as theoretical maximums, are aggregated in a stochastic analysis to quantify the energy efficiency and CO2 differences for BEV and FCEV energy systems. Carbon capture and storage improves source-to-wheels CO2 intensity for hydrogen produced from steam methane reformation (27 gCO2/km with carbon capture and store and 140 gCO2/km without for light-duty FCEVs). Light-duty BEVs have a lower CO2 intensity (11 gCO2/km) using decarbonised grid electricity and are 65% more efficient than light-duty FCEVs using grid energy. These effects translate to heavy-good vehicles but with added complexity. In a maximised trailer volume scenario, electric and fuel-cell heavy-good vehicles have similar projected carbon intensities from a natural gas primary energy source, but electric heavy-good vehicle using conventional battery systems or an electric road system are able to achieve a 55% and 67% carbon reduction (gCO2/m3 km) compared to fuel-cell heavy-goods vehicles, respectively.