The present invention relates to a composition for preventing and treating pancreatitis containing a naphthoquinone based compound or a pharmaceutically acceptable salt prodrug solvate or isomer thereof. Specifically it was verified that ß lapachone and dunnione which are the naphthoquinone based compounds decreased the ratio of pancreatic weight/body weight the pancreatic weight being increased by pancreatitis reduced the activity of increased digestive enzymes (amylase and lipase) and the expression of cytokines (IL 1ß (interleukin lß) and MCP 1) reduced or inhibited inflammation edema and cell necrosis of pancreatic tissues and suppressed the lung damage due to pancreatitis. Therefore the naphthoquinone based compound or the pharmaceutically acceptable salt prodrug solvate or isomer thereof can be favorably used for a composition for preventing and treating pancreatitis.