Energy system reliability and operational cost depend highly on the performance degradation experienced by system components. In complex systems, degradation of each single component affects matching and interactions of different system parts. Gas turbine fuel cell hybrid systems combine two different technologies to produce power with an extremely high conversion efficiency. Severe performance decay over time currently limits high temperature fuel cells lifetime; although at a different rate, gas turbine engines also experience gradual deterioration phenomena such as erosion, corrosion, and creep. This work aims at evaluating, for the first time, the complex performance interaction between degrading components in a hybrid system. The effect of deterioration in gas turbine pressure ratio and efficiency on fuel cell performance was analyzed, and at the same time, the impact of the degrading fuel cell thermal output on turbine blade aging was modeled to estimate a remaining useful lifetime.