Pantoprazole Vs. Omeprazole: What’s the Difference and Which Is Better for Treating Heartburn and GERD

By Jillian Foglesong Stabile MD, FAAFP, DABOM

August 20, 2025

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Prescription Drugs, Your Health & Wellness

Pantoprazole Vs. Omeprazole: What’s the Difference and Which Is Better for Treating Heartburn and GERD?

Pantoprazole and omeprazole are medications used to treat heartburn, gastroesophageal reflux (GERD), and even some types of stomach ulcers. If you’re suffering from one of these painful conditions that affect as many as 10-20% of people in the Western world (possibly as high as 28% in the United States), you may be looking for treatment options. When it comes to treatment options, pantoprazole vs. omeprazole is a common question. So, what is the difference, and which medication is better for treating heartburn and GERD? This guide will explore the similarities and differences between these two commonly used medications.



What is pantoprazole?

Pantoprazole is in a class of medications known as proton pump inhibitors (PPIs). Specifically, pantoprazole is in the benzimidazole subgroup of PPIs. Pantoprazole binds to hydrogen/potassium pumps in the stomach. This binding is irreversible, and the medication blocks acid secretion from the pumps for up to 24 hours after it is taken. Pantoprazole starts to work quickly and reaches its maximal effect within two to six hours.



What is omeprazole?

Omeprazole is also a proton pump inhibitor. Omeprazole takes effect quickly, within one hour of administration, and reaches its maximum effect in approximately 2 hours. Omeprazole binds irreversibly to the hydrogen/potassium pumps and will block acid secretion for up to 72 hours after it is taken, gradually decreasing back to normal by 5 days.



Why take pantoprazole vs omeprazole for treating gastritis?

Gastritis is a type of inflammation of the stomach. It can cause significant pain, though many people have mild symptoms or none at all. Gastritis can be caused by bacterial infection (H. pylori), certain autoimmune diseases, and the use of medications or chemicals. Gastritis can also be classified as acute or chronic. The stomach is a very acidic environment, and if there is inflammation in the stomach lining, the acid can exacerbate it. Pantoprazole and omeprazole are both used to decrease the amount of acid in the stomach to allow the lining to heal.



What is the difference between omeprazole and pantoprazole?

When choosing between pantoprazole and omeprazole, several factors should be considered. Your healthcare provider may recommend a specific medication based on your risk factors.

  Pantoprazole Omeprazole
Approved to treat: Erosive esophagitis (short and long term), GERD, Zollinger-Ellison syndrome Duodenal ulcer, H. pylori infection, Gastric ulcers, GERD, Erosive esophagitis (short and long term), Zollinger-Ellison syndrome, Multiple endocrine adenoma, systemic mastocytosis
Approved since: 2000 1989
Form Tablet, liquid, IV Powder, tablet, capsule, packet
Contraindications (absolute or relative) Allergy to medication, use of certain HIV drugs, Clostridium difficile infection, some types of fracture, lupus, stomach cancers, low magnesium levels Allergy to medication, use of certain HIV drugs, use of some blood thinners, osteoporosis, clostridium difficile infection, low magnesium, lupus, liver disease
Doses 20 mg or 40 mg 10 mg, 20 mg, or 40 mg
Availability Prescription only Over-the-counter and prescription
Can it be taken with food? Yes, with or without food is fine Recommended to take 30 minutes before meals



Is pantoprazole the same as omeprazole?

Pantoprazole and omeprazole have many similarities, but is pantoprazole the same as omeprazole? In short, no, they are not the same. The medications have slight differences in the conditions for which they are used, as well as reasons why they may not be the best choice for an individual patient. Pantoprazole is more likely to be used in a hospital setting because it is available in both IV and oral forms.



Is pantoprazole as good as omeprazole?

Pantoprazole is generally considered equal to omeprazole for treating several conditions. One study comparing omeprazole versus pantoprazole for the treatment of stomach ulcers and esophageal inflammation found that both medications were effective for treatment and had very few side effects, although omeprazole was more commonly used.



What side effects are common between pantoprazole and omeprazole?

Because the medications work similarly, the side effects between pantoprazole and omeprazole are similar. Common side effects between the two medications include:

  • Diarrhea
  • Headache
  • Respiratory infections
  • Abdominal pain

These side effects are common for other medications and are not limited to pantoprazole or omeprazole.



What side effects are not common between Omeprazole and Pantoprazole?

While the two medications share many side effects, there are also a few side effects that are not as common when comparing omeprazole vs pantoprazole. Pantoprazole can potentially cause long-term effects, including an increased risk of osteoporosis, vitamin and mineral deficiencies, small-intestinal bacterial overgrowth (SIBO), and diarrhea associated with certain conditions, such as Clostridium difficile (C. diff) infection and colitis. Omeprazole is more likely to cause flatulence, nausea and vomiting, decreased sensation, cough, rash, and dizziness, though these side effects are still very rare.



How successful is pantoprazole in treating gastritis and acid reflux?

Pantoprazole has been shown to have significant success rates in treating gastritis and acid reflux. A 2018 meta-analysis found that patients with erosive reflux had a higher response to treatment compared to those with reflux without erosions. The response rate in this study was 64-76%.



How successful is omeprazole in treating gastritis and acid reflux?

Similar to pantoprazole, omeprazole is also very effective in treating gastritis and acid reflux. A 2023 study looking at the effectiveness of omeprazole in acid peptic disease showed an improvement in reflux symptoms for 46-68% of patients between days 14 and 28.



Is pantoprazole better than omeprazole for heartburn and indigestion treatment?

Pantoprazole is very similar in its effectiveness to omeprazole for treating heartburn and indigestion. So, in many cases, there is no reason to consider switching from pantoprazole to omeprazole or vice versa. Depending on certain conditions, your healthcare provider may recommend one over the other. One study from the early 2000s found pantoprazole to be more effective than omeprazole in treating sleep problems related to GERD; however, the study compared dissimilar doses. Other studies have shown no difference between the two medications at dissimilar doses. Ultimately, the medicines are very similar and are often used interchangeably.



Omeprazole versus Pantoprazole FAQs

 

Which is safer, pantoprazole or omeprazole?

Pantoprazole and omeprazole are both very safe medications. There are a few reasons why one medication may be safer than another in certain circumstances.

Can you take omeprazole and pantoprazole together?

While your healthcare provider may occasionally recommend taking omeprazole or pantoprazole with other medications, including other antacids, it is not recommended to take omeprazole and pantoprazole together. Both medicines work similarly, so taking them together can increase the risk of side effects.

Is pantoprazole stronger than omeprazole?

Pantoprazole may be slightly stronger than omeprazole in some circumstances. Some studies have shown pantoprazole to be more effective than omeprazole in older individuals with esophageal inflammation. However, other studies have not shown a difference between the two medications.

Why is pantoprazole preferred over omeprazole?

Pantoprazole is preferred over omeprazole in specific cases for a few reasons. Omeprazole may decrease the effectiveness of certain medications, such as clopidogrel. Clopidogrel is a blood thinner that affects the platelets in the blood and is used in some people who have a history of heart attacks, coronary artery disease, or strokes. Because of the way that omeprazole is broken down in the body, it is more likely to decrease the effectiveness of clopidogrel than other PPIs such as pantoprazole.

Is pantoprazole 40 mg the same as omeprazole 20 mg?

As previously mentioned, mixed studies are showing the effectiveness of pantoprazole 40 mg and omeprazole 20 mg. Some studies have shown that pantoprazole 40 mg is more effective than omeprazole 20 mg, while other studies have found them to be similarly effective.

Can you take omeprazole and pantoprazole on the same day?

Because omeprazole and pantoprazole work similarly, you should not take both medications on the same day. Unless you are specifically advised to take both medicines by your healthcare provider, taking these medications on the same day may increase the risk of side effects. If you continue to experience symptoms, it is essential to consult your healthcare provider. They may recommend you take additional medications for your symptoms, or they may recommend further studies to evaluate whether your symptoms are due to another cause.



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Medications are expensive, and their costs can vary significantly between pharmacies, even those located across the street. If you are experiencing heartburn or other symptoms of reflux, or if your healthcare provider has recommended medication, you may be wondering how to save money on your prescriptions. Consider visiting us at WellRx. Some people save a little, while others save a lot. Prices vary across zip codes. Even pharmacies across the street from each other can have huge price differences. Our goal is to bring transparency to prescription medication pricing, enabling consumers to keep more money in their pockets. ScriptSave has been helping consumers save on their prescriptions for 25 years.

 

References

https://pmc.ncbi.nlm.nih.gov/articles/PMC8754510/

https://www.ncbi.nlm.nih.gov/books/NBK441938

https://www.ncbi.nlm.nih.gov/books/NBK499945/

https://www.ncbi.nlm.nih.gov/books/NBK539786/

https://www.drugs.com/medical-answers/pantoprazole-omeprazole-difference-between-3568252/

https://www.ncbi.nlm.nih.gov/books/NBK544250/

https://pubmed.ncbi.nlm.nih.gov/8180295/

https://tarbawej.elmergib.edu.ly/index.php/tarbawe/article/view/29/14

https://pubmed.ncbi.nlm.nih.gov/10705625/

https://pmc.ncbi.nlm.nih.gov/articles/PMC5894447/

https://pmc.ncbi.nlm.nih.gov/articles/PMC10428080/

https://journals.lww.com/ajg/fulltext/2004/10001/superiorityofpantoprazole40mg_versus.727.aspx

https://pmc.ncbi.nlm.nih.gov/articles/PMC4611579

https://pubmed.ncbi.nlm.nih.gov/14708472/

https://www.jacc.org/doi/abs/10.1016/j.jacc.2009.05.050

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