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An adaptive Fourier neural network (AFNN) control scheme is presented in this paper for the control of a class of uncertain nonlinear systems. Based on Fourier analysis and neural network (NN) theory, AFNN employs orthogonal complex Fourier exponentials as the activation functions. Due to the clear physical meaning of the neurons, the determination of the AFNN structure as well as the parameters of the activation functions becomes convenient. One salient feature of the proposed AFNN approach is that all the nonlinearities and uncertainties of the dynamical system are lumped together and compensated online by AFNN. It can, therefore, be applied to uncertain nonlinear systems without any a priori knowledge about the system dynamics. Derived from Lyapunov theory, a novel learning algorithm is proposed, which is essentially a frequency domain method and can guarantee asymptotic stability of the closed-loop system. The simulation results of a multiple-input-multiple-output (MIMO) nonlinear system and the experimental results of an X-Y positioning table are presented to show the effectiveness of the proposed AFNN controller.