d-Allulose (d-psicose) is a rare sugar, that contains no calories and exhibits 70% relative sweetness when compared with sucrose. Recently, several studies have demonstrated the anti-obesity effect of d-allulose, mediated by suppressing lipogenesis and increasing energy expenditure. Medium-chain triacylglycerols (MCTs) are lipids formed by 3 medium-chain fatty acids (MCFAs) with 6–12 carbon atoms attached to glycerol. MCTs have been expensively studied to reduce body fat accumulation in rats and humans. The anti-obesity effect of MCTs was not confirmed depending on the nutritional conditions because MCT might promote lipogenesis. In the present study, we examined the effects of simultaneous intake of diets containing low (5%) or high (13%) MCTs, with or without 5% d-allulose, on body fat accumulation in rats (Experiment 1). Furthermore, we assessed the interaction between 5% MCT and 5% d-allulose in the diet (Experiment 2). In Experiment 1, intra-abdominal adipose tissue weight was significantly greater in the high MCT diet groups than in the commercial diet (control) group. d-Allulose significantly decreased weights of intra-abdominal adipose tissue, carcass fat, and total body fat, however, these weights increased as the amount of MCT added increased. In Experiment 2, d-allulose significantly decreased almost all body fat indicators, and these values were not influenced by the presence or absence of MCT addition. The anti-obesity effect of d-allulose was observed with or without dietary MCT, and no synergistic effect was detected between d-allulose and MCT. These results suggest that d-allulose is a beneficial food ingredient in diets aimed at reducing body fat accumulation. However, further research is required on the synergistic effects between d-allulose and MCTs.