Uses of This Medicine. Pantoprazole is used to treat certain conditions in which there is too much acid in the stomach. It is used to treat erosive esophagitis or heartburn caused by gastroesophageal reflux disease (GERD), a condition where the acid in the stomach washes back up into the esophagus.his medicine may also be used to treat Zollinger Ellison syndrome, a condition where the stomach produces too much acid. Pantoprazole is a proton pump inhibitor (PPI). It works by decreasing the amount of acid produced by the stomach.