Purpose Previous studies showed that in the prevention of anterior cruciate ligament (ACL) injury, core muscles must be activated before lower limb movements in order to control the lower limb. The aim of this study was to investigate the improvement of lower limb muscle strength according to the number of weeks of core stability exercises in female athletes with and without a history of ACL injury. Methods Forty-two female athletes, 21 healthy and 21 with a history of ACL injury participated in this study. The number of weeks of core stability exercises included 1 week, 4 weeks, and 8 weeks. Subjects performed the training protocol three times a week and each session was about 45 min. Isometric strength of different muscle groups of the lower limb was measured before and after the completion of exercise weeks with Nicholas’s hand dynamometer. Results Findings indicated the number of weeks of core stability exercises had a significant effect on the strength of lower limb muscles [F (2, 01) = 371.87; p = 0.001]. Also, the number of weeks of core stability exercises had a significant effect on the strength of lower limb muscles in different groups [F (2, 01) = 49.61; p = 0.01]. In addition, the number of weeks of core stability exercises had a significant effect on the strength of different muscles of the lower limbs [F (3.27) = 551.67; p = 0.001] but, there was no significant difference in the strength of different muscles of the lower limbs in different groups [F (3.27) = 1.3; p = 0.27]. Furthermore, the number of weeks of core stability exercises had a significant effect on the strength of different muscles of the lower limbs in different groups [F (5.59) = 6.56; p = 0.001]. On the other hand, findings showed there was a significant difference between the two groups, and the group with a history of ACL injury had a more significant improvement [F (1, 38) = 9.9; p = 0.03]. Conclusions The number of weeks of core stability exercise had a significant effect on improving the strength of the lower limb muscles. These effects were different in healthy athletes and athletes with a history of ACL injury. As, in healthy athletes in some muscles such as the hamstring, there was a significant effect after 8 weeks only, while in athletes with a history of ACL injury, there was a significant effect after 1 week in all muscle groups. Therefore, it is recommended that therapists and sports trainers consider the optimal number of weeks of core stability exercise in the design of training programs for female athletes with and without a history of ACL injury.