As a result of the detailed site investigation performed for the design of a 4.3 km long tunnel, geological anomalies of four fault zones and a rock boundary were discovered on the tunnel route. Most of all, it was confirmed that pyrite, which may corrode steel material, is contained inside the geological anomalies, and pressured ground water flows out of the fault fractured zone. To overcome these geological conditions, antisulfur concrete for the concrete lining and anticorrosive swelling rock bolts are designed in the pyrite-containing sections. For the sections where a great amount of groundwater outflows, water blocking methods including grouting are applied according to the result of numerical analyses on the seepage. In addition, since the past earthquakes occurred around Korea have take place mainly near fault zones, seismic analyses were performed based on the Soil-Structure Interaction (SSI) concept and the strength of concrete tunnel lining is designed to be 27 MPa from 24 MPa in order to reinforce the tunnel structure.