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. Protonix (pantoprazole) is part of a group of medications called proton pump inhibitors (PPIs). Protonix uses include treating gastroesophageal reflux disease (GERD) and inflammation of the esophagus (esophagitis). Pantoprazole, sold under the brand name Protonix, among others, is a medication used for the treatment of stomach ulcers, short-term treatment of erosive esophagitis due to gastroesophageal reflux disease (GERD), maintenance of healing of erosive esophagitis, and pathological hypersecretory conditions including Zollinger–Ellison syndrome. [7. Find patient medical information for Pantoprazole (Protonix) on WebMD including its uses, side effects and safety, interactions, pictures, warnings, and user ratings Protonix (Pantoprazole) may treat, side effects, dosage, drug interactions, warnings, patient labeling, reviews, and related medications including drug comparison and health resources. Protonix is a proton pump inhibitor that decreases the amount of acid produced in the stomach. Protonix 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 (Protonix) is a medication that treats conditions that cause too much stomach acid, like heartburn, stomach ulcers and reflux disease. PROTONIX is indicated for maintenance of healing of erosive esophagitis and reduction in relapse rates of daytime and nighttime heartburn symptoms in adult patients with GERD. Controlled studies. 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. Prilosec (omeprazole) and Protonix (pantoprazole) are both proton pump inhibitors with several similarities: Both medications work by binding to the proton pump enzyme, H+/K+ ATPase, in the stomach lining.