Hormonal changes are caused by the menstrual cycle phases, which influence resting metabolic rate and eating behavior. The aim of the study was to determine resting metabolic rate (RMR) and its association with dietary intake according to the menstrual cycle phase in lean and obese Chilean women. This cross-sectional analytical study included 30 adult women (15 lean and 15 with obesity). Body composition was measured with a tetrapolar bioelectrical impedance meter. Nutritional status was determined by adiposity. A 24-h recall of three nonconsecutive days verifies dietary intake. The RMR was measured by indirect calorimetry. All measurements were performed in both the follicular and luteal phases of the menstrual cycle. Statistical analyses were performed with STATA software at a significance level, which was α = 0.05. The RMR (β = 121.6 kcal/d), temperature (β = 0.36 °C), calorie intake (β = 317.1 kcal/d), and intake of lipids (β = 13.8 g/d) were associated with the luteal phase in lean women. Only extracellular water (β = 1.11%) and carbohydrate consumption (β = 45.2 g/d) were associated in women with obesity. Lean women showed increased RMR, caloric intake, and lipid intake during the luteal phase. For women with obesity, carbohydrate intake increased but not RMR.