An exergoeconomic study of an ammonia-fed solid oxide fuel cell (SOFC) based combined system for transportation applications is presented in this paper. The relations between capital costs and thermodynamic losses for the system components are investigated. The exergoeconomic analysis includes the SOFC stack and system components, including the compressor, micro turbine, pressure regulator and heat exchangers. A parametric study is also conducted to investigate the system performance and costs of the components, depending on the operating temperature, exhaust temperature, and fuel utilization ratio. A parametric study is performed to show how the ratio of the thermodynamic loss rate to capital cost changes with operating parameters. For the devices and the overall system, some practical correlations are introduced to relate the capital cost and total exergy loss. The ratio of exergy consumption to capital cost is found to be strongly dependent on the current density and stack temperature, but less affected by the fuel utilization ratio.