A neural network based adaptive controller design method is proposed for reconfigurable flight control systems in the presence of variations in aerodynamic coefficients or control effectiveness decrease caused by control surface damage. The neural network based adaptive nonlinear controller is developed by making use of the backstepping technique for command following of the angle of attack, sideslip angle, and bank angle. On-line teaming neural networks are implemented to guarantee reconfigurability and robustness to the uncertainties caused by aerodynamic coefficients variations. The main feature of the proposed controller is that the adaptive controller is designed with assumption that not any of the nonlinear functions of the system is known accurately, whereas most of the previous works assume that only some of the nonlinear functions are unknown. Neural networks loam through the weight update rules that are derived from the Lyapunov control theory. The closed-loop stability of the error states is also investigated according to the Lyapunov theory. A nonlinear dynamic model of an F-16 aircraft is used to demonstrate the effectiveness of the proposed control law.