To know if the magnitude of change in resting metabolic rate (RMR) observed during an intervention is meaningful, it is imperative to first identify the variability that occurs within individuals from day to day under normal conditions. The 2 most common systems used to measure RMR involve a ventilated hood or a mouthpiece & nose clip to collect expired gases. The variation in measurement using these 2 approaches has not been systematically compared. RMR was measured in 10 healthy adults during 5 separate testing sessions within a 2‐week period where usual diet and physical activity were maintained. Each testing session consisted of one measurement of RMR using a ventilated hood system, followed by another using a mouthpiece & nose‐clip system. No significant difference in RMR was evident between measurement sessions using either indirect calorimeter. Oxygen consumption and RMR were significantly higher using the mouthpiece & nose‐clip system. Average within‐individual coefficient of variation for RMR was significantly lower for the ventilated‐hood system. RMR measures were consistently lower using the ventilated‐hood system by an average of 94.5 ± 63.3 kcal. Day‐to‐day variance was between 2% and 4% for both systems. The use of either system is appropriate for assessing RMR in clinical and research settings, but alternating between systems should be undertaken with caution. A change in RMR must be greater than ∼6% (96 kcal/d; 1.2 kcal/kg/d) or∼ 8% (135 kcal/d; 1.7 kcal/kg/d) when using a ventilated‐hood system or a mouthpiece & nose‐clip system, respectively, to observe any meaningful intervention‐related differences within individuals.