An apparatus and method aligning magnetically coupled inspection probes are provided. In this regard, a tracking probe may be magnetically coupled to a driven probe and move in coordination therewith. An alignment compensator for magnetically coupled inspection probes offsets misalignments between a driven probe and a tracking probe. Misalignments between magnetically coupled probes may be caused by gravity, friction, and movement of the probes. An alignment compensator may use one or more magnets, or electromagnets, to improve the alignment of the probes. An alignment compensator may include a control system for adjusting the power to an electromagnet or repositioning a magnet to offset misalignment of probes.