The ideal timing to implement anterior cruciate ligament injury prevention programs with respect to maturation is unclear. The purpose of this study was to investigate the effects of an injury prevention program on knee mechanics in early-, late-, and post-pubertal females. In the study, 178 adolescent female basketball players were assigned to six groups: early-pubertal training, early-pubertal control, late-pubertal training, and late-pubertal control, post-pubertal training, and post-pubertal control. The training groups performed an injury prevention program for six months. Medial knee displacement, knee flexion range of motion, and the probability of high knee abduction moment were assessed before and after the training period. After the six-month training period, medial knee displacement was significantly increased in the early-pubertal control group whereas it was unchanged in the early-pubertal training group. Knee flexion range of motion was significantly decreased in the early-pubertal control group whereas it did not change in the early-pubertal training group. The probability of high knee abduction moment was increased in the early-pubertal control group whereas it was unchanged in the earl-pubertal training group. The probability of high knee abduction moment was also decreased in the post-pubertal training group whereas it did not change in the post-pubertal control group. The program limited the development of high-risk movement patterns associated with maturation in early puberty while improving the knee mechanics in post-pubertal adolescents. Therefore, an injury prevention program should be initiated in early puberty and continue through the post-puberty years.