Background: To evaluate whether extracorporeal shock wave therapy (ESWT) in the pain point is a more effective treatment than the trigger point for myofascial pain syndrome (MPS) of the upper trapezius. Objects: The purpose of this study was to compare the most effective areas when applying extracorporeal shock wave therapy. Methods: A total of 30 patients with MPS were randomly assigned to the trigger point in the ESWT (n = 15) and pain point ESWT (n = 15) groups. Interventions in both groups were performed in one session, i.e., 2,000 shocks with 1.5 bar intensity. Pain and function were assessed using the visual analog scale (VAS) and cervical range of motion (ROM) and based on mechanical muscle properties. Statistical analysis was performed using the repeated measures two-way analysis of variance to determine the significance probability between pre- and post-test. Results: Changes in mechanical muscle properties were not statistically significant between the two groups. However, VAS and cervical ROM showed statistically significant differences at pre- and post-intervention, regardless of the group (p < 0.05). Conclusion: Although no significant difference was observed in the intervention effect, applying an extracorporeal shock wave to the pain point rather than the pain trigger point should be considered in order to save time in effectively and accurately identifying the pain trigger point and site.