In humans, the variation in resting metabolic rate (RMR) might be associated with health-related factors, as suggested by previous studies. This study explored whether the intra-assessment RMR variability (expressed as a coefficient of variation (CV; %)) is similar in men and women and if it is similarly associated with diverse health-related factors. The RMR of 107 young, and relatively healthy adults, was assessed using indirect calorimetry. Then, the CV for volumes of oxygen consumption (VO2) and carbon dioxide production (VCO2), respiratory exchange ratio (RER), and resting energy expenditure (REE) were computed as indicators of intra-assessment RMR variability. Body composition, cardiorespiratory fitness (peak VO2 uptake), circulating cardiometabolic risk factors, and heart rate and its variability (HR and HRV) were assessed. Men presented higher CVs for VO2, VCO2, and REE (all p </= 0.001) compared to women. Furthermore, in men, the intra-assessment RER variability was associated with vagal-related HRV parameters and with mean HR (standardized beta = -0.36, -0.38, and 0.41, respectively; all p < 0.04). In contrast, no associations were observed in women. In conclusion, men exhibited higher variability (CVs for VO2, VCO2, and REE) compared to women. The CV for RER could be a potential marker of cardiometabolic risk in young men.