An on-car brake lathe is provided with a runout compensation system configured to monitor the rotational position of a pair of slant discs within an aligning joint of the on-car brake lathe. The system monitors the amount of runout present between the rotating components of the on-car brake lathe and the wheel hub to which the on-car brake lathe is secured. The system calculates the appropriate rotational position for each slant disc within the aligning joint required to impart a necessary adjustment in the wheel coupling rotational axis in order to align the on-car brake lathe with the rotational axis of the wheel hub. Finally, an adjustment mechanism is activated to rotationally drive each slant disc directly to the calculated rotational position with a minimum amount of rotational movement based on the current rotational position of each slant disc and the required calculated rotational positions.