The autofocus is one of the important processes in the automated vision inspection or measurements using optical microscopes, because it influences the measuring accuracy. In this paper, we used the confocal microscope configuration based on not a pinhole but a single-mode optical fiber. A single mode fiber has the functions of source and detector by applying the reciprocal scheme. As a result, we acquired a simple system configuration and easy alignment of the optical axis. Also, we embodied a fast autofocus system by acquiring the focus error signal through a source modulation technique. The source modulation technique can effectively reduce physical disturbances compared with objective lens modulation, and it is easily applicable to general optical microscopes. The focus error signal was measured with respect to the modulation amplitude, reflectance of the specimen and inclination angle of the measuring surface. The performance of the proposed autofocus system was verified through autofocusing flat mirror surface. In addition, we confirmed that source modulation rarely degrades the depth resolution by the comparison between the FWHMs of axial response curves.