Resting metabolic rate (RMR) represents the largest component of total energy expenditure and is fundamental for estimating daily energy requirements in athletes. Although sex is commonly incorporated into predictive equations for RMR, the physiological determinants underlying sex differences remain incompletely understood. This study aimed to identify the body composition components associated with variation in RMR in male and female athletes and comparing the proportion of explained variance between sexes. This cross-sectional study included 74 male and 47 female Japanese athletes competing at the national level. Body composition was assessed using dual-energy x-ray absorptiometry. RMR was measured by indirect calorimetry using the Douglas bag technique under standardized fasting and resting conditions. Associations between RMR and body composition variables were evaluated using multiple regression models. Male athletes exhibited significantly greater fat-free mass (FFM) and skeletal muscle mass (SMM), and lower fat mass (FM) compared with female athletes. Absolute RMR was significantly higher in male athletes; however, RMR adjusted for FFM did not differ between sexes. Multiple regression analyses identified FFM as the primary predictive variable of RMR in both sexes, with SMM emerging as the significant variable when FFM was subdivided. The proportion of variance in RMR explained by these variables was higher in male athletes than in female athletes. The significant variables of RMR were either FFM or SMM, and were similar in Japanese male and female athletes, but their contributions differed between sexes. Sex differences in RMR may be partly attributable to differences in body composition and absolute body size. Given the cross-sectional design, these findings should be interpreted as associations rather than causal determinants.