Purpose: The aim of this study was to investigate within-cycle differences in nocturnal heart rate (HR) and heart rate variability (HRV) in naturally menstruating women (NM) and women using combined hormonal contraceptives (CU) or progestin-only hormonal contraceptives (PU). Methods: Physically active participants were recruited into three groups: NM (n = 19), CU (n = 11), and PU (n = 12). Participants' HR and HRV (with Bodyguard 2 HRV monitor) and blood hormones were monitored during one menstrual cycle (MC) (NM group) or for 4 wk (CU and PU groups). Estradiol, progesterone, and luteinizing hormone were analyzed from fasting blood samples collected four times in the NM (M1 = bleeding, M2 = follicular phase, M3 = ovulation, and M4 = luteal phase) and PU groups (M1 = lowest E 2 , M2 = M1 + 7 d, M3 = M1 + 14 d, and M4 = M1 + 21 d) and twice in the CU group (active and inactive pill phases). After every blood sample, nightly HR and HRV were recorded and examined as an average from two nights. Results: Hormonal concentrations differed (P < 0.05) between MC phases in the NM and PU groups, but not (P ≥ 0.116) between the active and the inactive phases in the CU group. In the NM and PU groups, some of the HRV values were higher, whereas in the NM group, HR was lower during M2 compared with M3 (P < 0.049) and M4 (P < 0.035). In the CU group, HRV values (P = 0.014-0.038) were higher, and HR was lower (P = 0.038) in the inactive phase compared with the first week of the active phase. Conclusions: The MC and the hormonal cycle phases influence autonomic nervous system balance, which is reflected in measurements of nocturnal HR and HRV. This should be considered when monitoring recovery in physically active individuals.