In high-performance concrete (HPC) subjected to high temperature during tunnel fires, the build-up of vapor pressure due to dehydration of the cement hydration products cannot be relieved due to the very low porosity and permeability of this type of concrete, often resulting in explosive spalling. Explosive spalling may cause devastating damage of the tunnel structure, which threatens both, civilians and emergency response units. This work suggests a potential application of silica aerogel in the protection of concrete linings, which consists in decorating the surface of HPC structures with a highly-insulating aerogel-cement mortar layer, with the aim of delaying the heating of the HPC and extending the performance of the main concrete structure of the tunnel under fire. The main aim of this study is investigating the impact of the microstructure, with special focus on the pore structure, on the thermal conductivity and the mechanical properties of the aerogel mortars. In particular, the integrity of the aerogels in the mortars, both in the mixing process and the possible long-term chemical degradation, was a main concern. Finally, a preliminary test of the performance against fire spalling was performed. While aerogel-containing mortars were able to protect HPC cubes from fire spalling under a specific thermal loading protocol, the thermal conductivity and the mechanical properties obtained were similar to those of cellular concrete in the same range of total porosity. A possible explanation of the lower-than-expected insulation performance is the partial degradation of the aerogel filler by reaction with the alkaline pore solution of the mortars. Implications of these new findings on aerogel-cement mixtures are also discussed.