Objective: This study aimed to systematically review and meta-analyze the effect of flywheel resistance training (FRT) versus traditional resistance training (TRT) on change of direction (CoD) performance in male athletes. Methods: Five databases were screened up to December 2021. Results: Seven studies were included. The results indicated a significantly larger effect of FRT compared with TRT (standardized mean difference [SMD] = 0.64). A within-group comparison indicated a significant large effect of FRT on CoD performance (SMD = 1.63). For TRT, a significant moderate effect was observed (SMD = 0.62). FRT of ≤2 sessions/week resulted in a significant large effect (SMD = 1.33), whereas no significant effect was noted for >2 sessions/week. Additionally, a significant large effect of ≤12 FRT sessions (SMD = 1.83) was observed, with no effect of >12 sessions. Regarding TRT, no significant effects of any of the training factors were detected (p > 0.05). Conclusions: FRT appears to be more effective than TRT in improving CoD performance in male athletes. Independently computed single training factor analyses for FRT indicated that ≤2 sessions/week resulted in a larger effect on CoD performance than >2 sessions/week. Additionally, a total of ≤12 FRT sessions induced a larger effect than >12 training sessions. Practitioners in sports, in which accelerative and decelerative actions occur in quick succession to change direction, should regularly implement FRT.