List of products in the National Drug Code with proprietary name . 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. It helps heal acid damage to the stomach and esophagus, helps prevent ulcers, and may help prevent cancer of the esophagus. Pantoprazole belongs to a class of drugs known as proton pump inhibitors (PPIs).