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This study explored the fatigue effect on postural control (PC) across menstrual cycle phases (MCPs) in female athletes. Isometric maximal voluntary contraction (IMVC), the center of pressure sway area (CoParea), CoP length in the medio-lateral (CoPLX) and antero-posterior (CoPLY) directions, and Y-balance test (YBT) were assessed before and after a fatiguing exercise during the follicular phase (FP), mid-luteal phase (LP), and premenstrual phase (PMP). Baseline normalized reach distances (NRDs) for the YBT were lower (p = 0.00) in the PMP compared to others MCPs, but the IMVC, CoParea, CoPLX, and CoPLY remained unchanged. After exercise, the IMVC and the NRD decrease was higher at PMP compared to FP (p = 0.00) and LP (p = 0.00). The CoParea, CoPLX, and CoPLY increase was higher in the PMP compared to FP (p = 0.00) and LP (p = 0.00). It was concluded that there is an accentuated PC impairment after exercise observed at PMP.