The objective of this work was to examine fuel cells as a possible alternative to the diesel fuel engines currently used in railway locomotives, thereby decreasing air emissions from the railway transportation sector. We have investigated the performance of a phosphoric acid fuel cell (PAFC) reactor, with n-hexadecane, C16H34 (a model compound for diesel fuel, cetane number = 100). This is the first extensive study reported in the literature in which n-hexadecane is used directly as the fuel. Measurements were made to obtain both polarization curves and time-on-stream results. Because deactivation was observed hydrogen polarization curves were measured before and after n-hexadecane experiments, to determine the extent of deactivation of the membrane electrode assembly (MEA). By feeding water-only (no fuel) to the fuel cell anode the deactivated MEAs could be regenerated. One set of fuel cell operating conditions that produced a steady-state was identified. Identification of steady-state conditions is significant because it demonstrates that stable fuel cell operation is technically feasible when operating a PAFC with n-hexadecane fuel.