<p>The present and future prospects of infrastructural development inevitably point towards underground structures. Tunnelling plays an important role in underground infrastructure projects, whose complexity increases with jointed or fractured rock. Discontinuities in rocks is common, such as joints, faults, folds, infilling weak materials, or other types of anisotropy. These discontinuities lead to uncertainties and failures in underground excavations. The most common type of discontinuity in the field is joints, which significantly affect the stress and deformation behaviour of the rock mass. Joints mostly occur as joint sets, which are usually parallel and equally spaced, and can also occur in multiple sets. This research simulated a 3D numerical model to investigate the effect of tunnel advancement on a raft foundation constructed on an anisotropic rock mass. Specifically, it analysed the deformation and stress responses of raft foundations and tunnels under different joint conditions during tunnelling. Moreover, the responses under different joint sets were compared, and the magnitude of the settlement was systematically evaluated. Results demonstrated that the presence and orientation of joints, particularly their inclination, significantly affect stress response during excavation. Active stress conditions occurred at the top and bottom of the tunnel, whereas passive conditions occurred on the lateral sides. In addition, the influence of tunnel advancement on stress distribution vanished at X/D = ≈ 3.5. These findings indicate that the structural orientation of an anisotropic rock layer significantly influences mat foundation behaviour. The most critical scenario occurred at a dip angle of 90°, where the maximum settlement reached 26% of the total raft foundation settlement.</p>