The aim of this study was to develop hydroponic-cultured ginseng vinegar (HGV) containing ginsenoside Rg2 in order to its anti-obesity and anti-hyperlipidemic effects in C57BL/6J mice. HGV was prepared by two-stage fermentation. The ginsenoside Rg2 contained in acetic acid-fermented HGV increased by 4.0 times compared to that in pre-fermented HGV. To measure the anti-obesity effect of HGV, thirty two mice were randomly divided into four groups: normal diet group (ND), high-fat diet group (HFD), high-fat diet-supplemented with HGV group (HGV), and high-fat dietsupplemented with green tea extract group (GT). Body weight, fat weight, and liver weight decreased in the HGV group. The HGV group also showed lower plasma levels of low-density lipoprotein (LDL)-cholesterol and triglycerides, and higher levels of high-density lipoprotein (HDL)-cholesterol compared to the corresponding levels in the HFD group. Furthermore, there were significant decreases in plasma aspartase aminotransferase (AST) and alanine aminotransferase (ALT) levels in the HGV group compared to the corresponding levels in the HFD group. These results suggest that HGV can be used as an anti-obesity therapeutic agent or functional ingredient.