Background and Purpose: Badminton is one of the most grueling sports requiring both high aerobic and anaerobic capacity of the athletes. Vertical jump is the basic task of the lower extremity when performing advanced overhead stroking. It is known that elite badminton players in Taiwan present superior hitting skills but often with poorer endurance during the games and thus influence their performance. However, the understanding of how fatigue would influence the vertical jump is limited. Thus, the purpose of the study was to investigate the changes of the body acceleration during vertical jumping after fatigue in elite high-school badminton players. Methods: A total of 26 elite badminton players from a senior high school were recruited. An inertial measurement unit (Xsens MTw Awinda) was secured at the level of L4-L5 to measure the acceleration of the whole body. Participants were required to perform 3 vertical jumps as high as possible before and after the fatigue protocol including a series of footwork, agility, and jumping tasks. Fatigue was defined if the finishing time of each series of protocol was 1.5 times longer than the first series. Mean (root mean square), peak, and rate of changes of the vertical acceleration were calculated for both squatting and jumping subphases. In addition, the jumping height was recorded and averaged. Paired t-tests or Wilcoxon signed rank tests were conducted. Results: The jumping height was significantly decreased after fatigue (51.74 ± 10.07 vs. 47.72 ± 10.07 cm, p = 0.001). During the squatting subphase, the mean, peak, and rate of changes of the downward acceleration were significantly increased (p = 0.002, p = 0.037, and p = 0.016, respectively) after fatigue. Although during the jumping subphase, no significant difference was found after fatigue. Conclusion: Decrease in jumping height after fatigue might be contributed from the larger and faster body acceleration in the downward direction during the squatting subphase implying poorer eccentric control or insufficient energy storage of the lower extremity might occur. Clinical Relevance: Current findings provide more information regarding the influence of fatigue on jumping mechanisms and indicate eccentric training of the lower extremity might be important for elite young badminton players.