Increasing fat burning during physical activity is thought to be an effective strategy for maintaining health and preventing lifestyle-related diseases, such as obesity and diabetes. In recent years, medium-chain triglycerides (MCTs) have gained attention as a dietary component for increasing fat-burning. However, this fat-burning effect has been unclear in people with high body mass index (BMI). Therefore, we aimed to clarify the effects of 2 g of daily ingestion of MCTs over 2 weeks on substrate oxidation during low-intensity physical activity in sedentary (i.e., with no exercise habit) subjects with a BMI from 25 (kg/m2) to less than 30, which is classified as obese in Japan. A placebo-controlled, randomized, double-blind, crossover study with a 2-week washout period was conducted. The rate of fat oxidation as well as the respiratory exchange ratio (RER) during exercise (with a cycle ergometer at a 20-watt load) were measured with a human calorimeter. MCTs ingestion significantly increased fat oxidation during physical activity and decreased RER compared to long-chain triglycerides ingestion. In conclusion, we suggest that daily ingestion of 2 g of MCTs for 2 weeks increases fat burning during daily physical activities in sedentary persons with a BMI ranging from 25 to less than 30.