Compare Pantoprazole vs. Omeprazole: Treatment, Side Effects, Cost

Written by Rebecca Farley | Reviewed by a licensed U.S. pharmacist | Posted March 03, 2021 | Updated October 18, 2021

Pantoprazole (Protonix) and omeprazole (Prilosec) are proton-pump inhibitors that treat various forms of gastrointestinal discomfort, including gastroesophageal reflux disease (GERD), heartburn, stomach ulcers, and esophagitis (inflamed esophagus). Omeprazole (Prilosec) is available as an over-the-counter medication while pantoprazole is not. Accordingly, pantoprazole is slightly more expensive, averaging nearly $500 for thirty tablets. The cheapest treatment option for GERD sufferers is generic prescription omeprazole, which can be as little as $2 for thirty units with the U.S. Discount Card. Of course, treatment depends on the condition: If you have occasionally persistent heartburn, you may opt for OTC omeprazole, which is relatively cheap. If symptoms persist, you may visit a provider, who can prescribe the cheaper OTC omeprazole. 

Comparing Pantoprazole vs. Omeprazole Prices

Drug Strength Quantity U.S. Average Retail Price U.S. Discount Card Price Lowest International Pharmacy Price Greatest Percentage Discount 
Prilosec Rx (Omeprazole)  10 mg 30 packets $411.39 $17.86 $34.31 N/A 
Prilosec OTC (Omeprazole) 20 mg  30 tablets  $22.72 N/A N/A N/A
Omeprazole OTC (generic) 20 mg 30 tablets  $23.50 N/A N/A N/A
Omeprazole (Generic)  20 mg  30 tablets $46.80 $2.40  $4.99 89%
Protonix  (Pantoprazole)  20 mg  30 tablets  $523.33 $491.51 $2.36  99%
Pantoprazole (Generic)  20 mg  30 tablets $80.77 $2.07 $5.23  98%

U.S. average prices according to GoodRx. U.S. Discount Card prices according to pharmacy discounts listed on near the zip code 10605. 

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What is the difference between OTC and prescription-only omeprazole? 

OTC omeprazole is a 14-day course of treatment for frequent heartburn. It comes only in 20 mg dosing because, without a doctor’s supervision, you are not equipped to select a dose concentration. Per the FDA, omeprazole OTC is better suited for people experiencing symptoms of esophageal inflammation like heartburn or gastrointestinal discomfort. Prescription omeprazole is better suited for those diagnosed with gastrointestinal issues that require long-term care. From a financial standpoint, prescription omeprazole is cheaper, especially if your symptoms persist. A $22 purchase every 14 days is more expensive than a $2 (with the U.S. Discount Card, per the chart) purchase every month. Without drug discount coupons, prescription omeprazole averages $40 for a month’s supply, not that much cheaper than OTC omeprazole. From PharmacyChecker’s perspective, omeprazole, a low-maintenance daily drug, is ideal for personal drug importation. Purchased at international pharmacies, prescription omeprazole is just $5. 

Omeprazole OTC comes in just 20mg doses, but prescription omeprazole ranges from 2.5 mg (in packet form) to 40mg. 

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Which is better: omeprazole or pantoprazole?

In a head-to-head study from 2003, neither omeprazole nor pantoprazole took the lead: Both drugs saw around a two-thirds success rate in their respective sample groups. The study did note that patients with high compliance had a higher chance of healing than patients who less rarely complied. Take that as a lesson: You have to take your medication as prescribed for it to work! 

As far as differences go, omeprazole is the older medication, having been approved in 1989. The FDA first approved pantoprazole nearly a decade later in 2000. In 2015, the FDA approved omeprazole (Prilosec) for over-the-counter treatment of frequent heartburn. Both medications are proton-pump inhibitors (PPIs); they prevent the production of stomach acid, essentially, so you don’t get all the bad side effects associated with it (heartburn, acid reflux, inflamed esophagus, GERD). They are not the only heartburn medications on the market, but they are considered the safest and most effective. 

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What are the side effects of omeprazole and pantoprazole? Does one have worse side effects?

For omeprazole, adverse reactions include “headache, abdominal pain, nausea, diarrhea, vomiting, and flatulence.” Pantoprazole’s side effects are similar, including “headache, diarrhea, nausea, abdominal pain, vomiting, flatulence, dizziness, and arthralgia.” Omeprazole does include risk of c. difficile-associated diarrhea (CDAD), a deeply uncomfortable and persistent gastrointestinal infection. C. diff is a common hospital-borne infection and a cause for concern; c. diff may be resistant to treatment, particularly if a patient has a long history of antibiotic use. The FDA has stated that it is “working with manufacturers to include information about the increased risk of CDAD with use of PPIs in the drug labels.” Currently, pantoprazole does not list c. diff infection as a potential adverse effect on its label. 

What are the side effects of omeprazole OTC? 

The FDA lists the following as potential side effects of omeprazole OTC: 

• headache

• diarrhea

• constipation

• upset stomach

• vomiting

• stomach pain

• cough

• cold symptoms

• dizziness

• rash

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What’s better: omeprazole, pantoprazole, or TUMs? 

TUMs are over-the-counter medications for immediate relief from heartburn symptoms. Omeprazole and pantoprazole (and other proton-pump inhibitors) treat the problem itself, reducing the amount of acid in your stomach. A pack of Prilosec purchased from a grocery store is meant to work over 14 days to reduce symptoms of aggressive stomach acid. Thus, Prilosec is not going to save you from your stadium hot dog. TUMs can. 

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How can I avoid heartburn?

Large meals, alcohol, caffeine, and tomato-adjacent meals (think pizza and marinara sauce) may cause heartburn. Mostly, alcohol is a major culprit in stomach acid issues. High alcohol consumption often accompanies a diagnosis of GERD (gastroesophageal reflux disease), a chronic illness that can result in respiratory issues. 

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Where are pantoprazole and omeprazole manufactured? 

Omeprazole sold in the U.S. is manufactured in Israel. Pantoprazole sold in the U.S. is made in India.

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