Fat oxidation (FAO) during aerobic exercise and whole-body FAO via lipid intake are thought to be important for the maintenance of health, such as the prevention of type 2 diabetes and obesity in sedentary persons in their 40s and 50s. Medium-chain triglycerides (MCTs) ingestion has been attracting attention. However, the effects of difference of sex and the composition of medium-chain fatty acids (MCFAs) are unclear, so we examined the effects of these factors on FAO during aerobic exercise. We conducted a randomized, double-blind, placebo-controlled, 3-arm, within-participants crossover trial. FAO during low- to moderate-intensity exercise was compared when octanoate-rich MCTs (C8R), decanoate-rich MCTs (C10R), or carbohydrate (control) was ingested. Three 2-week interventions were separated by two 2-week washout periods. An increase of FAO during exercise after the C8R diet was found in males, but not in females. An increase of carbohydrate oxidation (CAO) and oxygen uptake during exercise after the C10R diet was found in females, but not in males. In a pooled estimate of the effect of MCTs (C8R and C10R) in women and men, FAO increased during exercise. In conclusion, short-term ingestion of MCTs by middle-aged sedentary persons could increase FAO during aerobic exercise compared to carbohydrate ingestion, but the enhancing effect of MCTs on substrate utilization and oxygen uptake might vary, depending on sex and the composition of MCFAs.