Observations from past earthquakes have shown that subway tunnels can suffer severe damage or excessive deformation due to seismic shaking. This study presents the results of finite element analyses on subway tunnels installed in normally consolidated clay deposits subjected to far-field ground motions. The clay strata were modelled by a hyperbolic-hysteretic constitutive model. The influences of three factors on the seismic response of the clay-tunnel systems were examined, namely ground motion intensity, tunnel wall thickness and clay stiffness. Furthermore, the computed racking deformations of the tunnel were compared with several analytical estimations from the literature, and the relationship between racking ratio and flexibility ratio for rectangular tunnels installed in normally consolidated clay deposits was proposed. The findings may provide a useful reference for practical seismic design of tunnels.