Double-deck tunnels are an innovative tunnel design that has been recently implemented in some underground railways and metro lines worldwide. However, due to the complexity of this type of structures, its dynamic response has not yet been fully comprehended. This lack of understanding complicates the design of efficient vibration isolation countermeasures for them. Therefore, proper models for predicting the vibration impact of double-deck tunnels are highly needed. The aim of this paper is to present, on the one hand, an efficient model of a railway superstructure implemented in a double-deck tunnel and, on the other, to study how the vibration impact of this structure is affected by the addition of an elastomeric mat between the interior floor-tunnel contact and by modifications of the rail pads stiffness and damping values. In both cases, the results are presented in terms of the energy flow radiated upwards by the structure when harmonic moving loads circulate along the rails.