Female athletes are more prone to anterior cruciate ligament (ACL) injury than their male counterparts, presumably because of anatomical, hormonal, and neuromuscular differences. Of these three, only the neuromuscular component can be modified by preventive exercise. We aimed to evaluate the effect of a neuromuscular protocol on the prevention of ACL injury by performing meta-analysis, and to identify essential factors by subgroup analysis. An extensive literature review was conducted to identify relevant studies, and eventually, only seven randomized controlled trials or prospective cohort studies were included in the analysis. The odds ratios (OR) and the confidence interval (CI) for the overall effects of training and of potentially contributory factors were estimated. The OR and the 95% CI for the overall effect of the preventive training were 0.40 and [0.27, 0.60], respectively. Subgroup analysis revealed that an age under 18, soccer rather than handball, pre- and in-season training rather than either pre- or in-season training, and the plyometrics and strengthening components rather than balancing were significant. Meta-analysis showed that pre- and in-season neuromuscular training with an emphasis on plyometrics and strengthening exercises was effective at preventing ACL injury in female athletes, especially in those under 18 years of age. Further study is required to develop a relevant training program protocol of appropriate intensity.