DESC: Protonix (PANTOPRAZOLE) is a Proton Pump Inhibitor (PPI) used to treat ulcers, Gastroesophageal Reflux Disease (GERD), erosive esophagitis, or Zollinger-Ellison syndrome. This medicine works by blocking acid production in the stomach. It may be used in combination with antibiotics including amoxicillin or clarithromycin to treat certain types of ulcers. It may also be used to treat other conditions as determined by your doctor.