A method using artificial neural networks and inverse kinematics for machine tool error correction is presented. A generalized error model is derived, by using rigid body kinematics, to describe the error motion between the cutting tool and workpiece at discrete temperature conditions. Neural network models are then built to track the time-varying machine tool errors at various thermal conditions. The output of the neural network models can be used to periodically modify, using inverse kinematics technique, the error model’s coefficients as the cutting processes proceeded. Thus, the time-varying positioning errors at other points within the designated workspace can be estimated. Experimental results show that the time-varying machine tool errors can be estimated and corrected with desired accuracy. The estimated errors resulted from the proposed methodology could be used to adjust the depth of cut on the finish pass, or correct the probing data for process-intermittent inspection to improve the accuracy of workpieces.