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Purpose: This study aimed to examine the activities of heart rate variability (HRV) and cortisol secretion as markers of the autonomous nervous system (ANS) and the hypothalamic-pituitary-adrenal axis (HPA) during the menstrual cycle in female athletes. Method: Saliva samples of the participants (n = 28) were collected successively at 0, 15, 30, and 60 min after awakening to assess cortisol awakening response (CAR) during each of four phases of the menstrual cycle (the menstruation, ovulation, luteal, and premenstrual phases). Diurnal saliva samples were collected at noon, in the evening (17:00) and 22:00 for cortisol analysis. HRV was measured in the menstrual and premenstrual phases at rest (12:00-14:00). Results: There was no difference between CAR parameters in the menstrual phases. CAR parameters and diurnal cortisol levels were significantly correlated with each other throughout the menstrual cycle. Mean cortisol was a strong predictor of the area under the curve (AUC: S = 0.042; R-Sq = 98.4%). Time-dependent parameters of HRV (standard deviation of the N-N interval [SDNN; P = 0.049] and the root mean square of the successive R-R differences [rMSSD; P = 0.038]) were significantly higher in the menstrual phase. There were no correlations between CAR and HRV parameters. Conclusions: We suggest that the hypothalamic-pituitary-adrenal axis activity and the autonomic nervous system work in a separate manner that is not affected by the menstrual phases in sportswomen. The present study contributed to a better understanding of the relationship between the dynamics of cortisol release and the autonomic nervous system in different phases of the menstrual cycle in female athletes.