Patient instructed Protonix (pantoprazole) is a proton pump inhibitor that decreases the amount of acid produced in the stomach. Take once daily in the morning with or without food. Common Protonix side effects may include: headache, dizziness; stomach pain, gas, nausea, vomiting, diarrhea; joint pain; or fever, rash, or cold symptoms. Instructed to notify prescriber if unusual or bothersome side effects occur or medication is not effective.