Common
Gastrointestinal: abdominal pain (6%), diarrhea (9%), flatulence (4%), nausea (7%), vomiting (4%)
Neurologic: headache (12%), dizziness (3%)
Neuromuscular and skeletal: arthralgia (3%)

Rare
Gastrointestinal: constipation, dry mouth, hepatitis
Blood problems: low white blood cell count, thrombocytopenia
Immunologic: Stevens–Johnson syndrome, toxic epidermal necrolysis
Metabolic: elevated creatine kinase, elevated cholesterol levels, elevated liver enzymes (AST/ALT), swelling
Musculoskeletal: Muscle disorders, bone fracture and infection, Clostridium difficile infection, osteoporosis-related hip fracture, rhabdomyolysis
Kidneys: interstitial nephritis
Nutrition:  may reduce the absorption of important nutrients, vitamins, and minerals, including certain medications, leaving users at increased risk for pneumonia. Long-term use
Osteoporosis and bone fracture have been observed in people on high-dose and/or long-term (over one year) prescription proton pump inhibitors. Hypomagnesia has been observed in people on medications like pantoprazole when taken for longer periods of time (generally one year or more, although cases have been reported with regimens as short as three months). Deficiencies such as vitamin B12 deficiency, iron deficiency, and calcium deficiency may be seen with long term use. Vitamin B12 deficiency is due to the change in the acidic environment within the stomach with the use of pantoprazole which prevents peptidases from being activated. This prevents the cleaving of R-factor from vitamin B12 and prevents its absorption. Rebound hypergastrinemia may be seen when stopping the medication after long term use. Discontinuation
In people taking PPIs for longer than six months, a dose taper should be considered prior to discontinuation. For those on a moderate to high dose, this can be done by 50 percent every week until on the lowest dose. After a week it can then be stopped.
Pantoprazole, sold under the brand name Protonix, among others, is a proton pump inhibitor 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. It may also be used along with other medications to eliminate Helicobacter pylori. Effectiveness is similar to other proton pump inhibitors (PPIs). It is available by mouth and by injection into a vein.Common side effects include headaches, diarrhea, vomiting, abdominal pain, and joint pain. More serious side effects may include severe allergic reactions, a type of chronic inflammation known as atrophic gastritis, Clostridium difficile colitis, low magnesium, and vitamin B12 deficiency. Use in pregnancy appears to be safe. Pantoprazole is a proton pump inhibitor that decreases gastric acid secretion. It works by inactivating (H+/K+)-ATPase function in the stomach.Study of pantoprazole began in 1985, and it came into medical use in Germany in 1994. It is available as a generic medication. In 2020, it was the twentieth most commonly prescribed medication in the United States, with more than 26 million prescriptions. Medical uses
Pantoprazole is used for short-term treatment of erosion and ulceration of the esophagus for adults and children five years of age and older caused by gastroesophageal reflux disease. It can be used as a maintenance therapy for long-term use after initial response is obtained, but there have not been any controlled studies about the use of pantoprazole past a duration of 12 months.