Purpose: Fluctuating levels of endogenous estrogen are thought to have an adverse effect on lower limb biomechanics, given the observed higher rate of ACL injury at certain phases of the menstrual cycle. The purpose of this study was to investigate the effects of fluctuating endogenous estrogen levels during the menstrual cycle on acceleration transients at the proximal tibia in young physically active females. Methods: Eleven females aged 16–18 years participated in this study and were compared to a male control group. Female subjects were tested at each of the four phases of the menstrual cycle: menses, follicular, ovulation and luteal. On each test occasion, acceleration transients at the proximal tibia were measured while subjects performed an abrupt deceleration task (simulated netball landing). Results: No significant differences were found between the different phases of the menstrual cycle for peak tibial acceleration (PTA; P = 0.57), and time to zero tibial acceleration (TZTA; P = 0.59). However, there was a significant difference for time to peak tibial acceleration (TPTA) between menstruation and follicular (P = 0.04), menstruation and ovulation (P = 0.001), menstruation and luteal phase (P = 0.002), and follicular phase and ovulation (P = 0.007). In the male control group, no significant between-test session differences were observed for PTA (P = 0.48), TZTA (P = 0.08) and TPTA (P = 0.29). While there were no significant between-group differences for PTA (P = 0.21) and TZTA (P = 0.48), significant between-group differences were observed for TPTA (P = 0.001). Conclusion: The results of this project strongly suggest that serum estrogen fluctuations have an effect on tibial acceleration profiles in young female athletes during different phases of the menstrual cycle.