Due to increasing awareness of the deleterious environmental and health effects of diesel combustion emissions, major regulatory action and policy measures are focused on reducing emissions from diesel engines. Freight operations, including rail-based freight transportation, have received special attention as an industry where major change can be affected, especially in neighborhoods located near operations centers. A FORTRAN-based dynamic simulation model of an SOFC-GT (Solid Oxide Fuel Cell-Gas Turbine) system from a prior feasibility study has been adapted to analyze system operation along a representative but demanding route in southern California. In previous simulations with the model, the basic operational feasibility of the system has been demonstrated as well as the in-service operation for pre-reformed fuels. In the current study, the analysis is extended to include reformation of two fuels (diesel and natural gas) onboard the locomotive and analyses of system efficiency, fuel consumption, CO2 emission, and NOx emission that can be attained through careful thermal integration of the reformer unit. Route-averaged fuel-to-wheels system efficiencies of 60% and 52% are predicted for natural gas and diesel fuel, respectively. Additionally, SOFC-GT operation could provide (1) a reduction approaching 98% in NOx for both fuels; (2) a 54% savings in CO2 for operation on natural gas; and (3) a 30% CO2 reduction for operation on diesel fuel compared to state-of-the-art locomotive technology. These gains may be offset by design challenges, especially for the diesel case, due to the requirement for large volumes of water to support the reformation process even for medium-length freight hauling trips.