A Finite Element Analysis (FEA) investigation of concrete tunnel systems traversing seismic faults is carried out to determine how to effectively mitigate the stresses induced in the liner when subject to fault displacement. A parametric study of various fault parameters, both in the damage zone and competent rock, is carried out to determine the site conditions which induce the most stress on the tunnel liner system. Results indicate that friction angle, cohesion, and elastic modulus of fault zones have varying effects on the stresses induced on the liner. The width of damage zone and expected displacements are also investigated and it has been shown that even small displacements over narrow damage zones, around 10 m, can still result in significant damage to the concrete liner whereas in wider damage zones the effects of the displacement are more evident. The use of flexible joints in what is known as the articulated design method is investigated to mitigate the stresses induced by fault displacement and discussed. Several orientations, lengths and variations in relative stiffness of these flexible joints are investigated to determine their optimal effectiveness. Results show that this is an effective solution which can be used in design and repair of tunnels to mitigate the stresses and resulting damages to concrete tunnel liners subject to fault displacement.