The quadcopters are extremely sensitive to motor failures, which may occur secondary to broken propellers or motor faults during the flight operation. These faults alter the dynamics of the quadcopters, whereas the control algorithms generally used for controlling are no longer as effective. This paper presents a reliable fault-tolerant controller that can handle quadcopter motor failures in order to address these issues. The proposed control system uses a nonlinear disturbance observer-based sliding mode control (NLDO-SMC) to significantly manage the quadcopter’s rotational dynamics, while an integrated back-stepping controller (IBSC) is employed to supervise the translational movement. The developed nonlinear formulation’s NLDO-SMC, predicts motor failures and keeps the system resilient to unforeseen circumstances and disruptions that can arise while the vehicle is in the air. The suggested fault-tolerant control paradigm is validated by hardware-in-the-loop (HIL) experimental investigation and extensive simulations. The controller’s performance in real-world scenarios is thoroughly examined using the FPGA model. The results indicate that the controller can effectively deal with the effects of motor faults and restore control over the quadcopter’s stability. The proposed controller achieves robustness to up to 50% fault in a single motor, and the quadcopter follows the desired path with well-predicted rotation angles, thus proving the ability of the model to increase fault tolerance and operational safety under fault conditions.