Hydrogen potentially plays a key role in the transportation sector while transitioning to a net-zero emissions economy. Low-carbon hydrogen produced from fossil resources is often viewed as a bridge in the energy transition. This study comparatively evaluates life cycle greenhouse gas emissions of diverse pathways of fossil-based hydrogen production for fuel cell vehicle use. Life cycle emissions of hydrogen production alone vary significantly with production technology and are highly influenced by the supply sources of feedstock and electricity. Reforming and chemical looping with carbon capture and storage (CCS) are competitive to produce low-carbon hydrogen, whereas plasma pyrolysis is not competitive. Using low-carbon hydrogen to replace gasoline and diesel can significantly reduce life cycle emissions for light-duty and heavy-duty vehicles. Low-carbon hydrogen production by steam methane reforming, autothermal reforming, gasification, and chemical looping with CCS accounts for 64%–78% of the total life cycle emissions associated with hydrogen production, transport, leakage, and vehicle use. Although nominal hydrogen leakage alone has no remarkable effect on life cycle emissions, the expansion of assessment system boundary by including hydrogen transport and utilization can sizably elevate emissions. To secure short-term climate benefits for replacing diesel-fueled heavy-duty trucks and transit buses with hydrogen-fueled vehicles, however, it is necessary to simultaneously limit methane and hydrogen leakage along their supply and utilization chains. These findings imply that economic incentives and policies for a low-carbon hydrogen economy should be developed based on the life cycle emissions of both hydrogen production and utilization.