There have been few reports dealing with the drilling of printed wiring boards (PWBs) with micro-drills that are smaller than 0.2 mm in diameter, and super-high-speed spindles that are higher than 160,000 rpm. In these cases, preventing the micro-drill from breaking and keeping the position accuracy of the drilled hole has been difficult. We therefore focus on the high-speed step-drilling method and short stroke as a novel way of resolving these problems. On the other hand, determining the complicated combination of feed speed, rapid feed speed, and stroke length is difficult. Under these backgrounds, in this report we propose a fast-feed step cycle that use fast-feed command without the processing feed. Thus, we attempted to apply the response surface method to optimize these parameters. As a result, a proposed method was found to be effective to improve the drilled hole quality and drilling efficiency in such kinds of micro-drilling of the PWBs.