In a solid-oxide fuel cell system, the fuel cell stacks, the fuel reformer, tail gas combuster, heat exchangers, and fuel/air manifold, are contained in a "hot zone" within a thermal enclosure. A separate and larger structural enclosure surrounds the thermal enclosure, defining a "cool zone" outside the thermal enclosure for incorporation of "cool" components such as the air supply system and the electronic control system. To prevent unwanted temperature rise in the cool zone during shutdown, from residual heat escaping from the hot zone through the thermal enclosure, the structural enclosure is provided with vents through the lower and upper walls thereof to permit thermal convective circulation of air through the enclosure. The vents are baffled to prevent entry of splash and other contaminants, and the lower vent is provided with a float valve to prevent flooding of the enclosure in event of immersion of the SOFC system.