Enzymatically modified soybean oil with caprylic acid (SL), a physical mixture of tricaprylin and soybean oil (PHY), and soybean oil as control were fed (20% of diet weight) to female obese Zucker rats. Both lipids (SL and PHY) have similar total fatty acid composition containing 23.4 mol % caprylic acid (C8:0) but have different lipid structures. After 21 days of feeding, the body weight gain was 36.4% in the SL-fed group and 35.2% in the PHY-fed group, respectively; whereas the body weight of the control group increased 41.6%. Significant differences in the respiratory exchange ratio were observed between the SL and PHY groups. However, the contents of glucose, total and high density lipoprotein (HDL) cholesterol, and very low density and low density lipoprotein (VLDL + LDL) cholesterol in serum were not significantly different between the SL- and PHY-fed groups or among the three dietary groups (control, SL, and PHY) (p < 0.05). On the other hand, plasma total cholesterol and plasma triacylglycerol (TAG) were significantly higher in SL- and PHY-fed groups than in the control group. In the liver and inguinal adipocyte TAG, C8:0 was found in the SL-fed group, whereas it was not observed in the liver and inguinal adipocyte TAG of the PHY-fed group, which suggests that positional distribution of C8:0 of the TAG molecule is an important consideration in the metabolism of lipids. This study showed that different positional distribution in TAG molecules lead to different metabolic fates, resulting in the change of fatty acid composition in liver and inguinal adipose TAG in female Zucker rats.