Objective: Skeletal muscle function is vital for preventing injury during exercise. It has been reported that skeletal muscle function fluctuates with the menstrual cycle and is considered one of the causes of injury. This study aimed to clarify the relationship between muscle flexibility and muscle contraction characteristics and their changes with the menstrual cycle. Methods: The subjects were healthy women who voluntarily participated in the study through recruitment posters. Muscle flexibility was measured with the passive knee extension (PKE) test, isokinetic knee flexor strength, and the maximum muscle strength exertion angle under two conditions of 60°/s and 120°/s in dominant hamstrings. Additionally, their correlations were analyzed and compared between the menstrual and ovulatory phases. Results: Sixteen subjects (mean age: 20.56 ± 0.73 years; body mass index: 20.21 ± 1.60) participated in the study. Correlation analysis showed a significant negative correlation between PKE and the maximum muscle strength exertion angle under the condition of 60°/s during the menstrual phase (r = -0.54; p = 0.03). No significant difference was observed in the two-group comparison of the variables measured during the menstrual and ovulatory phases. Conclusion: This study confirmed that the more flexible muscles generate the maximum strength at a more contracted position during the menstrual phase in women. In the future, it is necessary to examine the relationship between the results of this study and exercise performance and injury occurrence.