In this paper the effect of systematic errors in gas temperature measurements on the thermal control of a Solid Oxide Fuel Cell system is demonstrated. Three control schemes were tested under two different conditions. First, the real gas temperature at the point of interest was used as input for the controller. Second, the reading of the thermocouple that takes the measurement at the same point was used as input. The second approach included the bias on the measurement due to radiation and heat conduction on the thermocouple. The results showed an overestimation of temperatures with important influence on the system control. Furthermore, in one case the system could not follow the required power demand and it failed. A successful solution to the problem was obtained by increasing the dimension of the system's heat exchanger. (C) 2013 Elsevier B.V. All rights reserved.