In this paper, a direct adaptive fuzzy neural network (DAFNN) controller for trajectory tracking control of the non-linear non-affine pneumatic servo system is presented. First, using a neural network identifier, the non-linear dynamics of a real pneumatic servo system is simulated. By comparing the output of the neural network and the output of the experimental setup, it is observed that the non-linear pneumatic actuator system is well-identified using neural networks. By incorporating the Lyapunov stability theorem, the adaptive laws for the parameters of the controller are obtained, parameter boundedness and stability of the closed-loop system are guaranteed. Finally, practical results are successfully implemented for trajectory tracking control of the pneumatic servo system, in which the effect of the simultaneous updating of the antecedent and consequent’s parameters of the fuzzy neural network controller has been investigated. The tracking error ±1.3mm and ±1 mm for proposed updating method compared to ±2.5mm and ±3.5mm, for a case that the weigh parameters are merely adjusted, are obtained. The results indicate the proposed adjustment method improves the performance of the controller in the presence of unknown nonlinearities and dynamics uncertainty.