The seismic response of tunnels constructed in a deposit of granular soil of depth greater than 20 m is examined in this paper. Three-dimensional discrete-element method (DEM) simulations were used to model the soil assembly and the tunnel lining. Soil particles were simulated as rigid spherical particles that are allowed to overlap at the contact points. The tunnel lining was modeled as a flexible system using a collection of particles that were glued together using cementitious bonds to mimic the physical properties of an actual tunnel. Free-field boundaries were utilized at the model’s lateral sides to prevent the propagating wave’s reflections back to the domain and enforce the free-field motion. The DEM computational framework was validated using published centrifuge test results. DEM simulation results reveal good agreement with the experimental centrifuge test results when subjected to the same input motion. Further simulations were carried out to investigate the seismic response of the system under different input motion characteristics. The dynamic earth pressure was monitored at certain points on the tunnel lining. It was found that the dynamic earth pressure and tunnel lining forces increased during seismic excitation and the final residual values were, in most cases, considerably larger than the initial static values. The results also showed that the maximum amplification factor, ground settlement and tunnel lining internal forces occurred close to the resonant frequency of the system.