This paper presents an investigation of fuel cell systems consisting of a hydrogen fuel cell and a bottoming power cycle in which the energy of waste heat is recovered. Starting from thermodynamics and the reversible limit, we examine the efficiency of the conversion of fuel cell systems as a function of temperature. Practical fuel cell systems are examined here first by using simple assumptions for the loss functions. These are later refined by using experimentally determined performance equations for a molten carbonate fuel cell (MCFC) stack. The temperature dependence of the efficiency of the total MCFC systems is predicted and analyzed. Within practical limits, the operating temperature of the fuel cell has only a minor impact on the overall system efficiency. This provides a degree of freedom in the optimization of other performance parameters such as endurance and cost.