The CFD model of the train-tunnel system, previously developed on proven analytical dependencies, is improved by the introduction of a tunnel cross-passage and the consideration of surface roughness. These additions bring the simulation setup closer to real conditions allowing to explore the FDS features in the evaluation of the aerodynamic effects occurring in a tunnel. Pressure and velocity patterns are obtained for the resulting model of a high-speed train in a tunnel with a cross-passage. The maximal and minimal pressure levels for the tunnel and the cross-passage spans are calculated to provide the data for the design phase and safety assessment. The approach to determine the most loaded surfaces of the tunnel and its inner structures, e.g. escape doors, for an estimation of their operational reliability is discussed. The study shows that the FDS software can be a helpful tool in assessing scenarios where the train-tunnel interaction is reviewed, though its applicable capabilities and set of features are largely dependent on the tasks to solve and need to be accurately adjusted.