Obesity is an epidemic condition resulting from energy imbalance. Rats artificially selected for low intrinsic aerobic capacity (low capacity runners - LCR) do not require hyperphagia to induce their obese phenotype. We have demonstrated that both male and female high-capacity runners (HCR) are more physically active and eat more food than LCR during both ad libitum and calorie restricted feeding. HCR lose more weight under 50% calorie restriction, which also suppresses their high physical activity (PA), suggesting that the HCR metabolism is less thrifty than LCR. Here, we find that a variation of calorie restriction--long-term intermittent feeding (IF), where female rats are fed ad lib every other day--stimulates a greater amount of weight and fat loss in the obesity-prone LCR. This treatment makes them nearly indistinguishable from their lean HCR counterparts in body weight and composition. In contrast, HCR females lose predominantly lean mass during IF. Most surprisingly, after 3 months on IF, LCR are able to eat more food, compared to their first 2 weeks of IF, to maintain their reduced body weight. HCR show a pronounced alternating pattern of physical activity, with high PA on fed days and suppressed PA on fasting days. Although LCR on IF still display a lower amplitude of PA than HCR, they have increased PA over ad libitum -fed LCR, especially on fed days. Another similar rat model based on artificial selection of high vs. low response to exercise training does not show the same segregated response to long-term IF as do rats artificially selected for intrinsic aerobic capacity (HCR/LCR). The metabolic response to a limitation in distribution or quantity of calories such as IF is dependent on intrinsic aerobic capacity, and is distinct from the response to standard calorie restriction, suggesting that dietary interventions should be adjusted by phenotype.