The a-C:H:Zr-x coatings are deposited on micro-drills using a closed field unbalanced magnetron (CFUBM) sputtering system with pulsed-DC power frequencies in the range 30 kHz to 110 kHz (the x in the term a-C:H:Zr-x is the frequency varied in the deposition process). The hardness of the various coatings is systematically explored. Additionally, the machining performance of the coated micro-drills is investigated by conducting high-speed through-hole drilling tests utilizing Printed Circuit Board (PCB) specimens. The experimental results reveal that the a-C:H:Zr-70 coating has the highest hardness (42 GPa), while the a-C:H:Zr-110 coating has the lowest hardness (26 GPa). In addition, it is shown that the a-C:H:Zr-70 coating increases the life of the micro-drill by a factor of three compared to that of an uncoated micro-drill.