The Bahce-Nurdag tunnel, which is the longest railway tunnel in Turkey with approximately 10 km was planned as two tubes. During the excavation of the second tube starting from the Nurdag portal, the tunnel-boring machine (TBM) jammed at 1267 m of the excavation. The second tube was abandoned due to TBM jamming, and it was decided to build a third tube. For this construction, additional portal and tunnel excavations were needed. These excavations resulted in additional stresses. Moreover, the project was constructed in a highly seismically active region. For this purpose, the tunnel portal section was investigated numerically by finite-element analysis. Considering the results obtained from the three-dimensional (3D) numerical analysis, the existing portal was enlarged and excavation of the third tube was started. Currently, the portal construction was successfully completed, and the third tube was excavated for approximately 2200 m with the TBM. It was concluded that the suggested methodology with the excavation and support systems was found satisfactory when the analysis results were compared with in situ conditions. This study suggests that multiple tunnels and large portals to be constructed in highly seismically active regions be simulated by 3D numerical analysis for successful construction.