A neural network based adaptive reconfigurable flight controller is presented for a class of discrete-time nonlinear flight systems in the presence of variations of aerodynamic coefficients and control effectiveness decrease caused by control surface damage. The proposed adaptive nonlinear controller is developed making use of the backstepping technique for the angle of attack, sideslip angle, and bank angle command following without two time separation assumption. Feedforward multilayer neural networks are implemented to guarantee reconfigurability for control surface damage as well as robustness to the aerodynamic uncertainties. The main feature of the proposed controller is that the adaptive controller is developed under the assumption that all of the nonlinear functions of the discrete-time flight system are not known accurately, whereas most previous works on flight system applications even in continuous time assume that only the nonlinear functions of fast dynamics are unknown. Neural networks learn through the recursive weight update rules that are derived from the discrete-time version of Lyapunov control theory. The boundness of the error states and neural networks weight estimation errors is also investigated by the discrete-time Lyapunov derivatives analysis. To show the effectiveness of the proposed control law, the approach is i]lustrated by applying to the nonlinear dynamic model of the high performance aircraft.