This paper describes the development of a neural network (NN) based adaptive flight control system for a high performance aircraft. The main contribution of this work is that the proposed control system is able to compensate the system uncertainties, adapt to the changes in flight conditions, and accommodate the system failures. The underlying study can be considered in two phases. The objective of the first phase is to model the dynamic behavior of a nonlinear F-16 model using NNs. Therefore a NN-based adaptive identification model is developed for three angular rates of the aircraft. An on-line training procedure is developed to adapt the changes in the system dynamics and improve the identification accuracy. In this procedure, a first-in first-out stack is used to store a certain history of the input-output data. The training is performed over the whole data in the stack at every stage. To speed up the convergence rate and enhance the accuracy for achieving the on-line learning, the Levenberg-Marquardt optimization method with a trust region approach is adapted to train the NNs. The objective of the second phase is to develop intelligent flight controllers. A NN-based adaptive PID control scheme that is composed of an emulator NN, an estimator NN, and a discrete time PID controller is developed. The emulator NN is used to calculate the system Jacobian required to train the estimator NN. The estimator NN, which is trained on-line by propagating the output error through the emulator, is used to adjust the PID gains. The NN-based adaptive PID control system is applied to control three angular rates of the nonlinear F-16 model. The body-axis pitch, roll, and yaw rates are fed back via the PID controllers to the elevator, aileron, and rudder actuators, respectively. The resulting control system has learning, adaptation, and fault-tolerant abilities. It avoids the storage and interpolation requirements for the too many controller parameters of a typical flight control system. Performance of the control system is successfully tested by performing several six-degrees-of-freedom nonlinear simulations.