The ultrasonic horn used for bonding of flip chip has been designed to vibrate at a natural frequency. The ultrasonic horn must be manufactured accurately in physical terms, because the small change of mechanical properties may result in the significant change of natural frequency. Therefore, tight tolerance is inevitable to keep the natural frequency in acceptable range. However, since tightening of the tolerance increases the manufacturing cost significantly, trade-off between the cost and accuracy is necessary. In this research, an attempt was made to design the ultra sonic horn within acceptable natural frequency while the manufacturing cost was kept as low as possible. For this purpose, among the 18 tolerances of physical terms of the ultrasonic horn, the most important 4 factors were selected using Taguchi method. The equation to relate those main factors and the natural frequency was made using response surface method. Finally, optimal design scheme for minimum manufacturing cost without a loss of performance was determined using SQP method.