Context: The indirect markers of muscle damage have been previously studied in females. However, inconclusive results have been found, possibly explained by the heterogeneity regarding monitoring and verification of menstrual-cycle phase. Purpose: To determine whether the fluctuations in sex hormones during the menstrual cycle influence muscle damage. Methods: A total of 19 well-trained eumenorrheic women (age 28.6 [5.9] y; height 163.4 [6.1] cm; weight 59.6 [5.8] kg body mass) performed an eccentric-based resistance protocol consisting of 10 × 10 back squats at 60% of their 1-repetition maximum on the early follicular phase (EFP), late follicular phase, and midluteal phase of the menstrual cycle. Range of motion, muscle soreness, countermovement jump, and limb circumferences were evaluated prior to 24 and 48 hours postexercise. Perceived exertion was evaluated after each set. Results: Differences in sex hormones indicated that tests were adequately performed in the different menstrual-cycle phases. Prior to exercise, muscle soreness was higher in the EFP (4.7 [7.7]) than in the late follicular phase (1.1 [3.2]; P = .045). No other variables showed significant differences between phases. Time-point differences (baseline, 24, and 48 h) were observed in knee range of motion (P = .02), muscle soreness, countermovement jump, and between sets for perceived exertion (P < .001). Conclusion: Although the protocol elicited muscle damage, hormonal fluctuations over the menstrual cycle did not seem to affect indirect markers of muscle damage, except for perceived muscle soreness. Muscle soreness was perceived to be more severe before exercise performed in EFP, when estrogen concentrations are relatively low. This may impair women’s predisposition to perform strenuous exercise during EFP.