The present invention relates to a composition for the prevention and treatment of pancreatitis comprising a naphthoquinone-based compound, a pharmaceutically acceptable salt, a prodrug, a solvate, or an isomer of the same. Particularly, the naphthoquinone-based compounds β-lapachone and dunnione can reduce the pancreatic weight/body weight ratio, which is increased by pancreatitis; reduce the increased activities of digestive enzymes (amylase and lipase); reduce the expressions of cytokines (IL-1β (interleukin-1β) and MCP-1); reduce or inhibit the inflammation, edema, and cell necrosis of the pancreatic tissues; and inhibit the lung damage caused by pancreatitis. Therefore, the naphthoquinone-based compound, the pharmaceutically acceptable salt, the pro-drug, the solvate, or the isomer thereof can be effectively used as a composition for the prevention and treatment of pancreatitis.