Aim of this work is to model and study the behavior of thermocouples as they are used in the measurement of gas temperatures in solid oxide fuel cell systems. Due to the high temperature regime in such systems, the effect of radiation and conduction from surrounding solids may bias the measurements with important consequences on control, performance, and cell durability. In order to study these effects a mathematical model of a working thermocouple was developed and it was integrated in that of a heat exchanger, which was part of a larger SOFC system. The enhanced heat exchanger's model was then validated with measurements from a test on a real system. The possibility to overcome the bias and to have a more correct approximation of the real gas temperatures is discussed.