A system and method are provided for exchanging heat in fuel cell systems (100) in which the anode and cathode off-gases are provided with separated flow paths. In one embodiment, where a fuel cell stack (110) has separate anode and cathode off-gas flow paths, separate anode off-gas from the at least one fuel cell stack (110) and at least one heat transfer fluid are passed through a first heat exchange element (126) to exchange heat between the anode off-gas and the heat transfer fluid. The cathode off-gas exiting the at least one fuel cell stack is then combined with the anode off-gas from the heat exchange element (126) in a burner and burned.