An apparatus and method for calibrating a 3D position in a 3D position and orientation tracking system are provided. The apparatus according to an embodiment may track the 3D position and the 3D orientation of a remote device in response to a detection of a pointing event, may acquire positions pointed to by the laser beams, in response to the detection of the pointing event, may generate a 3D reference position, based on information about the pointed to positions and the tracked 3D orientation, may calculate an error using the reference position and the tracked 3D position, and may calibrate the 3D position to be tracked, using the error.