As various healthcare technologies such as regenerative medicine, precision medicine, and alternative approaches to animal testing develop, the interest in the use and application of nano- and microfibers is steadily increasing. In this study, the effect of parylene-C coating on electrospun fibers was investigated, and a pattern coating method was developed to expand the potential utilization of parylene-C-coated electrospun fibers. An SEM analysis demonstrated that parylene-C was successfully deposited on the electrospun fibers without any failure such as pinholes or air bubbles. Biocompatibility was investigated through cell tests, which indicated that the coated fibers were non-toxic and supported cell growth well. Tensile tests demonstrated a significant increase in the elastic modulus of the parylene-C-coated fibers, with it nearly quadrupling compared to the original PCL fibers, and the fracture strength almost doubled. At the same time, hydrophobicity was well maintained without any statistically significant changes. In particular, a non-adhesive magnet–metal masking was proposed in order to selectively coat the electrospun fibers with parylene-C with a specific pattern. Furthermore, it was presented that the magnet–metal mask-based coating electrospun nanofibers with parylene-C could be used in the fabrication of hybrid fibers composed of different diameters and materials.