This study presents a transformer-based approach for fault-tolerant control in fixed-wing Unmanned Aerial Vehicles (UAVs), designed to adapt in real time to dynamic changes caused by structural damage or actuator failures. Unlike traditional Flight Control Systems (FCSs) that rely on classical control theory and struggle under severe alterations in dynamics, our method directly maps outer-loop reference values -- altitude, heading, and airspeed -- into control commands using the in-context learning and attention mechanisms of transformers, thus bypassing inner-loop controllers and fault-detection layers. Employing a teacher-student knowledge distillation framework, the proposed approach trains a student agent with partial observations by transferring knowledge from a privileged expert agent with full observability, enabling robust performance across diverse failure scenarios. Experimental results demonstrate that our transformer-based controller outperforms industry-standard FCS and state-of-the-art reinforcement learning (RL) methods, maintaining high tracking accuracy and stability in nominal conditions and extreme failure cases, highlighting its potential for enhancing UAV operational safety and reliability.