Learn about the side effects of pantoprazole, from common to rare, for consumers and healthcare professionals. 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. Pantoprazole is used to treat certain stomach and esophagus problems (such as acid reflux). It works by decreasing the amount of acid your stomach makes. This medication relieves symptoms such as heartburn, difficulty swallowing, and persistent cough. Pantoprazole (Protonix) is a medication that treats conditions that cause too much stomach acid, like heartburn, stomach ulcers and reflux disease. Pantoprazole is a proton-pump inhibitor (PPI) and its effectiveness is similar to that of other PPIs. [10] It is available by mouth and by injection into a vein. Pantoprazole, brand name Protonix, is a drug that belongs to the class of drugs called proton pump inhibitors (PPIs). Protonix is used for the treatment of GERD (gastroesophageal reflux disease), stomach (peptic) and duodenum ulcers, and Zollinger-Ellison syndrome. Pantoprazole (Protonix) is a proton-pump inhibitor (PPI). It's used to treat symptoms of gastroesophageal reflux disease (GERD) in adults and children. It's also used to treat other conditions involving too much stomach acid, such as erosive esophagitis, in adults only. Overview: Pantoprazole is used to treat acid reflux and other conditions where you have too much acid in your stomach. It works by reducing how much acid your stomach makes and usually takes a. Pantoprazole is a proton pump inhibitor that decreases the amount of acid produced in the stomach. Pantoprazole is used to treat erosive esophagitis (damage to the esophagus from stomach acid caused by gastroesophageal reflux disease, or GERD) in adults and children who are at least 5 years old. 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 (the tube between the throat and stomach) in adults and children 5 years of age and older.