Women of childbearing age have variations in substrate oxidation rates that can lead to overweight, type II diabetes, and other conditions that may be associated with metabolic inflexibility and the variations in estrogen concentrations observed during the monthly ovarian cycle. PURPOSE: This study aimed to verify and compare the influence of eight treadmill high-intensity interval training (HIT) sessions on carbohydrate and lipid oxidation rates (CHOox and LIPox, respectively) and intensities of ventilatory anaerobic thresholds (VATs) of women in different phases of the monthly ovarian cycle. METHODS: Eleven irregularly active women performed incremental treadmill exercise testing followed by submaximal work-rate running for 45 min to determine VATs, VO2peak, peak velocity (Vpeak), and substrate oxidation rates, before and after a training period, in different phases of their monthly ovarian cycle (follicular phase group, FL, n = 6; luteal phase group, LT, n = 5). The training period consisted of eight HIT sessions, composed each one of eight sets of 60 s running at 100%Vpeak interspersed by 75 s recovery every 48 h. RESULTS: Our results showed no significant differences in VATs intensities between groups. The comparison between groups showed significant differences in relative energy derived from CHO pre- and post-training of -61.42% and -59.26%, respectively, and LIP pre- and post-training of 27.46% and 34.41%, respectively. The relative energy derived from CHO after the training period was 18.89% and 25.50% higher for FL and LT, respectively; consequently, the relative energy derived from LIPox after the training period was 8,45% and 3.46% lower for FL and LT, respectively. Over the training period, Vpeak was ~13.5 km/h, which produced the relative intensities of ~89%VO2peak e ~93%HRpeak for both groups. CONCLUSION: The monthly ovarian cycle phases promote significant changes in substrate oxidation rates leading to a decrease in CHOox. High-intensity interval training can minimize the differences observed and constitute an alternative intervention.