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Purpose: The purpose of this study was to investigate the effect of whole-body vibration training on the flexibility and agility of professional soccer players. Methods: Sixteen professional soccer players participated voluntarily in the study. Subjects were allocated to two groups: the experimental group received whole-body vibration (WBV) and team training, and the control group received only team training. Team training was conducted in 15 sessions of 70 min duration over 3 weeks. WBV training was applied at 40 Hz frequency, 5 sets (1 min-training, 1 min-resting) in a squatting position. Outcomes from sit-and-reach, side-step test, burpee test, and T-test were measured before and after training. To examine pre- and post-intervention differences between the two groups, a paired t-test was used. Independent t-tests were performed to compare pre- and post-test scores and the time difference of the two groups. Results: Significant improvements in sit-and-reach and agility variables were observed in the experimental group (p < 0.05). In particular, flexibility (sit-and-reach) and agility (the side-step test and the burpee test) were significantly different between the two groups (p < 0.05). Conclusion: These findings suggest that whole-body vibration training has a positive effect on performance enhancement for professional soccer players.