Pantoprazole is a proton pump inhibitor that decreases the amount of acid produced in the stomach. Pantoprazole is used to treat damage from gastroesophageal reflux disease (GERD), a condition in which backward flow of acid from the stomach causes heartburn and possible injury of the esophagus. It is also used to treat conditions where the stomach produces too much acid, such as Zollinger-Ellison syndrome.