During the past few years, design of experiments (DOE) has been gaining acceptance in the telecommunications research community as a mean for designing and analyzing experiments economically and efficiently. In addition, the need for introducing a systematic robust design methodology (i.e., one of the most popular DOE methodologies) to network simulations has been increasing. In this paper, we present an architecture of voice over IP (VoIP) application and the E-Model for calculating the perceived quality of service (QoS). Then, we apply the Taguchi robust design methodology to optimize the perceived QoS of VoIP application, and describe the detailed step-by-step procedures. We have used ns-2 simulator to collect experimental data in which the SN ratio, a robustness measure, is analyzed to determine an optimal design condition. The analysis shows that "initial delay time in playout buffer" is a major control factor for ensuring robust behaviors of the perceived QoS of VoIP. Finally, we verify the proposed optimal design condition using a confirmation experiment.