This crossover study protocol examines whether menstrual cycle phases influence resting energy expenditure and the thermic effect of high-fat meals in 12 premenopausal women aged 18-30. Participants will undergo metabolic testing during both early follicular and mid-luteal phases, measuring energy expenditure, substrate oxidation rates, appetite markers, and key hormones estradiol and progesterone. The research addresses conflicting findings in the literature about hormonal influences on metabolism. Understanding menstrual cycle impacts on energy metabolism could significantly improve metabolic research design in premenopausal women, where hormonal fluctuations are often overlooked as confounding variables. If phase-dependent differences emerge, this could explain inconsistencies across nutrition studies and suggest timing considerations for metabolic interventions. The findings may also inform personalized nutrition approaches, particularly for weight management strategies that account for cyclical metabolic variations. However, the small sample size of 12 participants limits generalizability, and this represents only a protocol paper—actual results remain pending. As this is a preprint awaiting peer review, the methodology and eventual findings require validation through the peer review process before clinical applications can be considered.