Recently, an incremental type sensor based backstepping (SBB) control approach, based on singular perturbation theory and Tikhonov’s theorem, has been proposed. This Lyapunov function based method uses measurements of control variables and less model knowledge, and it is not susceptible to the model uncertainty caused by fault scenarios. In this paper, the SBB method has been implemented on a fixed wing aircraft with its focus on handling structural changes caused by damages. A new hybrid autopilot flight controller has been developed for a Boeing 747-200 aircraft after combining nonlinear dynamic inversion (NDI) with SBB control approach. Two benchmarks for fault tolerant flight control (FTFC), named rudder runaway and engine separation, are employed to evaluate the proposed method. The simulation results show that the proposed control approach leads to a zero tracking-error performance in nominal condition and guarantees the stability of the closed-loop system under failures as long as the reference commands are located in the safe flight envelope.