PURPOSE: To examine the incidence of injuries among different menstrual phases in eumenorrheic cycles and abnormal menstrual cycles in female athletes. METHODS: This prospective cohort study recruited female athletes involved in collegiate, semi-professional, or professional team sports. Participating athletes self-reported their menstruation during the follow-up period. Menstrual cycles were classified as polymenorrhea, oligomenorrhea/amenorrhea, and eumenorrhea. Eumenorrheic cycles were further divided into estimated follicular phase (EFP), estimated ovulatory phase (EOP), and estimated luteal phase (ELP). Time-loss injuries and sports participation status were recorded by team medical staff. Incidence rates for each cycle and phase category were calculated per 1,000 athlete-days with 95% confidence intervals (CI). Incidence rate ratios (IRR) were utilized to compare risks among cycle and phase categories. RESULTS: Data from 316 female athletes were analyzed over a median follow-up period of 337 days. The incidence rates during eumenorrheic, oligomenorrheic/ amenorrheic, and polymenorrheic cycles were 3.10 (95% CI, 2.61-3.67), 2.11 (95% CI, 1.44-2.98), and 4.84 (95% CI, 2.77-7.86) per 1,000 athlete-days, respectively. Among eumenorrheic phases, the highest incidence rate was in the EOP at 5.14 (95% CI, 3.26-7.7), followed by the EFP at 3.19 (95% CI, 2.47-4.04) and the ELP at 2.52 (95% CI, 1.85-3.35). The incidence rate ratios (IRRs) for EOP compared to EFP and ELP were 1.61 (95% CI, 1.004-2.586) and 2.04 (95% CI, 1.238-3.357), respectively. CONCLUSIONS: Injury risk is significantly higher during the EOP compared to the EFP and ELP in eumenorrheic cycles. Injury incidence was found to be lower during oligomenorrheic/amenorrheic cycles than during eumenorrheic cycles. Future studies should explore the factors contributing to the heightened injury risk during the EOP and the observed reduction in injury rates during oligomenorrheic/amenorrheic cycles.