Previous studies reported the impact of intrinsic and extrinsic factors on intraoperative hypothermia. However, no clinical study to date has considered the effects of both the phase of the menstrual cycle (an intrinsic factor) and the fresh gas flow rate (FGF) during anesthesia (an extrinsic factor) on the core body temperature and intraoperative hypothermia. This study is aimed at investigatig the effect of the menstrual cycle phase on intraoperative hypothermia when considering the FGF in patients who underwent laparoscopic gynecologic surgery. This study included 667 women aged 19-65 years with menstruation cycles and menopause. The patients were divided into the follicular, luteal, and menopause groups. The primary outcome was the correlations of hormonal status with intraoperative hypothermia. Secondary outcomes included the incidence of intraoperative hypothermia, time to onset of hypothermia, incidence of shivering after anesthesia, and frequency of antishivering drug use in the three groups and risk factors for hypothermia. Overall, the hypothermia incidence was the lowest and the time to onset of hypothermia was the longest in the luteal phase group. At a high FGF, the incidence of hypothermia in the luteal phase group was lower than that in the other two groups (
P
<
0.05
). At a low FGF, the time to onset of hypothermia in the luteal phase group was longer than that in the other two groups (
P
<
0.05
). The female hormonal status had weak positive correlations with hypothermia at low and high FGF rates. A high FGF in univariate and multivariate analyses, follicular phase and menopause in multivariate analysis, and estradiol and progesterone levels in univariate analysis were risk factors for hypothermia. When considering the FGF, the luteal phase is associated with better outcomes concerning intraoperative hypothermia.