Pantoprazole: everything you need to know

last updated: Dec 06, 2021

5 min read

If frequent heartburn and burning chest pain sound familiar, you might be searching for some relief. Pantoprazole, a medication that reduces the amount of acid in the stomach, may help.


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What is pantoprazole? 

Pantoprazole (brand name Protonix) is a proton pump inhibitor (PPI), a type of medication used to reduce the amount of acid in the stomach. Most frequently, this drug is used for the treatment of a condition called gastroesophageal reflux disease (GERD), also known as acid reflux. 

It’s also used to treat peptic ulcer disease and a rare condition known as Zollinger-Ellison syndrome. Keep reading to learn everything you need to know about pantoprazole, what it’s used for, and the kinds of side effects some people experience when taking it.

How the medication works

Our stomachs help us digest food by producing acid, which breaks down what we eat into smaller, more easily processed bits. This acid is very corrosive, and the stomach has special protections, so it doesn’t get damaged by the acid it produces. 

Unfortunately, there are some situations where these protections are not enough. If there is too much acid, if the protective layers of the stomach are damaged, or if the acid somehow escapes the stomach and goes up into the esophagus (the tube connecting your mouth and stomach), it can cause serious damage and pain. 

Pantoprazole and all of the other PPIs work by turning off the production of gastric acid in your stomach, effectively reducing the amount of acid there and preventing or alleviating these often painful symptoms like heartburn, regurgitation, sore throat, and stomach pain (Wolfe, 2020). 

When is it prescribed?

If you’re living with a condition like chronic heartburn or PUD, pantoprazole or another PPI may be prescribed. Let’s take a closer look at common health conditions pantoprazole can help treat. 

Acid reflux (GERD)

Acid reflux, also known as GERD, is when stomach acid goes up into the esophagus. The most common symptoms of GERD include (Vakil, 2006):

  • Heartburn: This is a feeling of discomfort or pain in the middle of your chest that usually appears after you eat.

  • Bad breath: You may notice a sour taste in your mouth (especially after lying down or waking up in the morning).

  • Regurgitation: This is when you can feel food rising back up into your throat. It’s often accompanied by a sour taste in your mouth.

Occasional episodes of heartburn that last for a short period after meals are typically not a cause for concern. Treatment involves taking a PPI like pantoprazole when symptoms arise. If these episodes become frequent and uncomfortable, your healthcare provider may recommend that you undergo a more thorough investigation. 

This is especially true if the acid reflux is frequent (with more than two episodes per week). That’s because frequent reflux can cause a condition called Barrett’s esophagus, which results from repeated exposure of the esophagus to stomach acid, causing damage to the cells there. This condition is quite common, affecting between 10–20% of people in the Western world (Dent, 2015). 

While some people experience no symptoms at all, others experience pain or difficulty when swallowing, bloody coughs, bloody stool, iron-deficiency anemia, or weight loss. If you are experiencing these symptoms, your healthcare provider might recommend evaluation using an upper endoscopy and a barium swallow test. 

During an upper endoscopy, a tiny camera is inserted through your mouth or nose down your throat to look at your esophagus and your stomach. During a barium swallow, you will be asked to swallow a substance called barium while x-rays are taken. This allows your healthcare provider to see the shape and structure of your esophagus and identify any problems that might be contributing to your symptoms. 

Peptic ulcer disease

Peptic ulcer disease (PUD) develops when there is an injury to the lining of the stomach or small intestine. These injuries are called ulcers. Damage is typically caused by an infection with  Helicobacter pylori (or H. pylori for short) or from consistent use of over-the-counter pain medications known as non-steroidal anti-inflammatory drugs (NSAIDs). These include common household medications like aspirin (brand names Advil and Motrin) and others. 

The most common symptom of peptic ulcers is pain in the upper abdomen. For many people, the pain comes as attacks, often with long, symptom-free periods between episodes. Depending on where the ulcer is located, some people report that eating makes the pain worse, and others report that eating actually alleviates the symptoms. 

Some patients have no pain at all, in which case, your healthcare provider might suspect PUD if you have: 

  • Low iron levels in your blood (iron-deficiency anemia

  • Signs of bleeding in your digestive system (like blood in your stool, black stools, or small amounts of blood in your stool detected on a routine screening test).

How PUD is treated depends on the cause. To identify the cause, your healthcare provider will likely ask you questions about your habits (for example: Have you taken a lot of pain medication recently?). To diagnose H. pylori, your healthcare provider can do a simple breath test called the urea breath test or check your stool for the bacteria. If you have been taking pantoprazole to treat your symptoms, you will have to stop taking it before the test (since it can cover up the sign of infection). 

Treatment for H. pylori typically involves the use of two types of antibiotics to clear the infection and a PPI like pantoprazole or omeprazole, which both help to alleviate the discomfort associated with H. pylori infections and help to get rid of the infection along with antibiotics (Chiba, 2013). 

Treatment typically lasts 10–14 days. While your symptoms may resolve before you finish the full course of treatment, it’s very important to continue taking the treatment for as long as your healthcare provider has recommended. This ensures that the infection is treated completely and reduces the chance that it will return (Crowe, 2020).

For patients who are diagnosed with peptic ulcers caused by NSAIDs, you’ll be instructed to stop using those medications and switch to an alternative option. Treatment of PUD caused by NSAIDs also involves the use of PPIs to alleviate the symptoms and help the ulcers to heal (Vakil, 2020). 

Zollinger-Ellison syndrome (ZES)

ZES is a rare condition in which small growths—known as gastrinomas—form in the pancreas or the upper part of the small intestine. It occurs in just one out of every four million people every year. 

Gastrinomas produce too much of a substance called gastrin. Gastrin tells the stomach to start producing stomach acid. People with ZES have so much stomach acid that they tend to develop ulcers in their stomach/small intestine. Symptoms can include: 

  • Peptic ulcer disease

  • Heartburn

  • Abdominal pain

  • Diarrhea

  • Blood in the stool. 

If your healthcare provider suspects that you have ZES, they can do a simple blood test to measure gastrin levels in your blood. Treatment can involve the use of PPIs like pantoprazole and removing the growths causing the condition, if possible.

Side effects of pantoprazole

The most frequently reported side effect of treatment with pantoprazole is a headache. Other side effects include:

  • Diarrhea

  • Nausea

  • Abdominal pain

  • Gas

Rarely, pantoprazole can cause dizziness or muscle pain. 

Reduced levels of stomach acid can make it difficult for your body to absorb certain nutrients. The most common nutrient that people can’t absorb properly while taking pantoprazole is magnesium, but a deficiency typically only occurs in people taking PPIs for more than three months. Magnesium deficiency can result in muscle spasms, cramps, or weakness.

Less frequently, people on long-term treatment with pantoprazole lasting more than two years can develop a vitamin B12 deficiency. Your healthcare provider can check your B12 levels using a simple blood test and recommend supplements (either in the form of pills or injections) if necessary.

Drug interactions

PPIs in general have a risk for multiple drug interactions. More serious reactions caused by the following medications should be avoided while taking pantoprazole:

  • Atazanavir

  • Nelfinavir

  • Erlotinib

  • Rilpivirine

Keep in mind this is not a comprehensive list of all drugs that cause severe reactions. Speak with your healthcare provider about any medications you are taking before starting a new treatment.

Warnings and risks

In rare cases, PPIs can cause a rare allergic reaction known as acute interstitial nephritis, which affects the kidneys. Symptoms can include nausea and vomiting, or peeing a lot less than usual. If you have ever had this reaction before, tell your healthcare provider. 

Long-term use of PPIs like pantoprazole can harm the balance of bacteria in the digestive system and result in an infection called Clostridium difficile (or C. diff for short). This condition is most common among hospitalized patients, and the most prominent sign of this infection is persistent diarrhea. 


If you have any medical questions or concerns, please talk to your healthcare provider. The articles on Health Guide are underpinned by peer-reviewed research and information drawn from medical societies and governmental agencies. However, they are not a substitute for professional medical advice, diagnosis, or treatment.

How we reviewed this article

Every article on Health Guide goes through rigorous fact-checking by our team of medical reviewers. Our reviewers are trained medical professionals who ensure each article contains the most up-to-date information, and that medical details have been correctly interpreted by the writer.

Current version

December 06, 2021

Written by

Yael Cooperman, MD

Fact checked by

Mike Bohl, MD, MPH, ALM

About the medical reviewers

Yael Cooperman is a physician and works as a Senior Manager, Medical Content & Education at Ro.

Dr. Mike is a licensed physician and a former Director, Medical Content & Education at Ro.