Active faults present significant challenges to tunnel safety, especially in long-distance projects where avoiding fault zones is often not feasible. Current engineering practices employ four primary structural strategies to mitigate fault-induced damage, frequently combining multiple methods. However, these approaches largely depend on engineering experience rather than comprehensive theoretical models. This study investigates the headrace tunnel of the Kohala Hydropower Project in Pakistan, which traverses the Himalayan Frontal Thrust (HFT) active fault zone. Numerical models were developed to assess the effectiveness of flexible joints and composite linings in mitigating fault-induced deformations. Through orthogonal experimental design, optimal structural parameters were identified to enhance tunnel safety by reducing the internal forces of the structure by approximately 80% under fault movement. The results offer practical design and construction recommendations for tunnels in seismically active regions.