Soybean is known to have an anti-obesity effect. We compared the anti-obesity effect of doenjang, a fermented soybean paste, with that of nonfermented soybeans in rats. Steamed soybeans and doenjang (steamed soybeans fermented and aged for 10 months) were sampled and freeze-dried. Male Sprague-Dawley rats were fed basal (BA) (5% fat), high fat (HF) (30% fat), HF+steamed soybeans (SOY), or HF+doenjang (DJ) diet ad libitum for 8 weeks. HF significantly increased body weight gain, liver weight, hepatic triglyceride (TG) and cholesterol levels, and epididymal fat pad weight compared with BA. Compared with HF, body weight gain and hepatic TG and cholesterol levels were significantly lower in SOY and DJ groups, but they were not significantly different from each other. DJ significantly reduced visceral fat weight and epididymal adipocyte size compared with HF, whereas SOY resulted in a mild reduction without significance. This was possibly because DJ showed lowered fatty acid synthase (FAS) activity and elevated carnitine palmitoyltransferase (CPT)-1 activity in liver tissue more than SOY. SOY and DJ did not affect serum total and high-density lipoprotein-cholesterol levels compared with HF; however, DJ significantly lowered the atherogenic index and serum leptin level. In conclusion, doenjang, a fermented soybean product, was more effective than soybeans for preventing diet-induced visceral fat accumulation, possibly because of its greater effects on CPT-1 activity stimulation and FAS activity suppression. These effects may be due in part to the higher content of aglycone isoflavones in doenjang.