Studies examining the impact of menstrual cycle phases on the cardiac autonomic nervous system have produced inconsistent results. This study aimed to investigate this relationship, controlling for the confounding effects of diet, physical activity, and sleep, which can be affected by the menstrual cycle. Fifteen female college students with regular menses were enrolled. Data regarding 24-h heart rate variability (HRV), dietary intake, eating behavior, menstrual distress, and sleep and activity parameters were obtained during the follicular and luteal phases. Power spectral analysis of HRV was used to calculate low-frequency (0.04-0.15 Hz, LF), high-frequency (>0.15 Hz, HF), and total spectral power (TP). Cardiac sympathetic and parasympathetic nervous system activity indicators were evaluated as LF/HF and HF/TP, respectively. Intake of protein and fat, as well as total sleep time and number of awakenings, were higher in the luteal phase than in the follicular phase (p<0.05). Tendencies for increased mean activity counts, emotional eating scores, and behavioral change scores in the Menstrual Distress Questionnaire were observed in the luteal phase (p<0.10). Although LF/HF was higher in the luteal phase (p=0.036), the relationship was weakened after controlling for diet, physical activity, and sleep (p=0.113). Our findings suggest that altering sympathetic nervous system activity during the menstrual cycle was not independent from major lifestyle factors (diet, physical activity, and sleep). Menstrual cycle phase and changes of these parameters should be considered when assessing the cardiac autonomic function among menstruating woman.