Palpation is a standard clinical tool to diagnose abnormal stiffness changes in soft tissues. However, it is difficult to palpate the supraspinatus muscle because it locates under the trapezius muscle. The magnetic resonance elastography (MRE) uses harmonic mechanical excitation to quantitatively measure the stiffness (shear modulus) of both the superficial and deep tissues. The purpose of this study was to build a vibration system for applying the MRE to the supraspinatus muscle. In this study, a power amplifier and a pneumatic pressure generator were used to supply vibrations to a vibration pad. Six healthy volunteers underwent MRE. We investigated the effects of position (the head of the humerus and the trapezius muscle) of the vibration pad on the patterns of wave propagation (wave image). When the vibration pad was placed in the trapezius muscle, the wave images represented clear wave propagation. On the other hand, when the vibration pad was placed in the head of the humerus, the wave images represented unclear wave propagation. This result might be caused by wave interferences resulting from the vibrations from bones and an intramuscular tendon of the supraspinatus muscle. The mean shear modulus also was 8.12 ± 1.83 (mean ± SD) kPa, when the vibration pad was placed in the trapezius muscle. Our results demonstrated that the vibration pad should be placed in the trapezius muscle in the MRE of the supraspinatus muscle.