Technological progress and market expansion in the semiconductor industry require ultra-precise and high-speed processing and motion systems. However, even though reaction force compensation (RFC) linear motor motion stages help reduce the transmitted reaction force, the residual vibration of the movable magnet track after motion acts as a disturbance, affecting settling time and tracking performance. To address this issue, this study introduces a fuzzy neural network controller for an RFC linear motor motion stage. Since non-linear factors, such as frictional forces from guide rails, make it difficult to accurately model the system, a Nonlinear Autoregressive Neural Network (NARX) is used to identify the nonlinearity from displacement and servo control outputs. The fuzzy logic controller, which takes into account the error and error rate, is then combined with the inverse model controller of NARX. Finally, the fuzzy neural network controllers are integrated with the existing PIV (proportional-integral-velocity) control in feedforward configurations. The experiments demonstrate the potential performance improvements of the proposed approach over the PIV controllers.