The abnormal content of blood lipids often results in metabolic diseases, such as hyperlipidemia and obesity. Many agents, including natural sources from traditional food, have been developed to regulate the blood lipid contents. In this study, we examined the anti-hyperlipidemic activity of Rhynchosia nulubilis seeds pickled with brown rice vinegar (RNSpBRV), a Korean traditional pickled soybean food. Since RNSpBRV is made of R. nulubilis seeds (RNS) soaked in brown rice vinegar (BRV), we compared the anti-adipogenic activity between RNS, BRV and solid fraction of RNSpBRV (SF-RNSpBRV), liquid fraction of RNSpBRV (LF-RNSpBRV). For this, the inhibitory effect of lipid accumulation in 3T3-L1 adipocyte was checked by adding methanol extracts of mixed RNS and BRV, LF-RNSpBRV, and SF-RNSpBRV. The addition of each methanol extract up to 1 mg/ml showed no cytotoxicity on 3T3-L1 adipocyte, and approximately 20% of the lipid droplet formation was suppressed with the methanol extract of BRL or SF-RNSpBRV. The highest suppression (42.1%) was achieved with LF-RNSpBRV. In addition, mice fed a high fat diet (HFD) supplemented with 5% RNSpBRV powder led to increased high density lipoprotein (HDL) cholesterol and lower blood glucose, triglyceride, and total cholesterol compared to mice fed with a HFD diet only. Interestingly, the size of the epididymis cells gradually decreased in HFD + 1% RNSpBRV and HFD + 5% RNSpBRV-fed mice if compared those of HFD-fed mice. Taken together, these results provide evidence that RNSpBRV has a regulatory role in lipid metabolism that is related to hyperlipidemia.