If you have been prescribed naproxen, you may be worried about the effect on your stomach. Naproxen is effective for pain, but like other anti-inflammatory painkillers it can irritate the stomach, and it is often prescribed alongside a second medicine, usually omeprazole, to protect against that.
This guide explains what naproxen does to the stomach and gut, why omeprazole is so often prescribed with it, what you can do to protect your digestive health, and where a gut microbiome test may help you understand your own symptoms. It is for information only. It is not a reason to stop or change any medicine, and if naproxen is upsetting your stomach the right step is to speak to your GP or pharmacist.
What is naproxen?
Naproxen is a painkiller that belongs to a group of medicines known as non-steroidal anti-inflammatory drugs (NSAIDs). It is widely used to relieve pain and inflammation from conditions like arthritis, injuries, period pain, and musculoskeletal problems. Naproxen is known for being fast-acting and long-lasting.
But while NSAIDs like naproxen are effective for pain, they are also associated with disruption to the gut, particularly with long-term use. This includes irritation of the stomach lining and, further down, changes in the gut microbiome.
What does naproxen do to the stomach?
Research has shown that regular use of NSAIDs like naproxen can cause peptic ulcer disease, a condition where painful ulcers develop in the stomach lining or the first part of the small intestine (Drini M (2017). Peptic ulcer disease and non-steroidal anti-inflammatory drugs. Australian Prescriber. https://pubmed.ncbi.nlm.nih.gov/28798512/).
This happens because NSAIDs interfere with the stomach's natural defences. They reduce prostaglandins, the compounds that normally protect the stomach lining by:
- Reducing acid production
- Promoting mucus and bicarbonate secretion
- Supporting blood flow to the stomach lining
Without this protection, stomach acid can damage the lining, increasing the risk of ulcers, inflammation, and digestive discomfort.
Symptoms that may point to gut irritation from naproxen include:
- Heartburn
- Stomach pain
- Nausea or vomiting
- Indigestion
- Diarrhoea
If you have a history of stomach ulcers or digestive problems, tell your GP or pharmacist before taking naproxen or any NSAID.
Can you take naproxen with omeprazole?
Yes. Omeprazole, a proton pump inhibitor (PPI), is very commonly prescribed alongside naproxen precisely to protect the stomach. PPIs work by reducing how much acid the stomach produces, which lowers the risk of the ulcers and irritation that NSAIDs can cause. This is a standard and well-established combination, not a sign that anything has gone wrong.
NICE prescribing guidance recommends that people taking an NSAID who are at higher risk of gastrointestinal problems, for example older adults or those with a history of ulcers, should also be offered a PPI such as omeprazole to protect the stomach.
What can you take with naproxen to protect your stomach?
For most people who need that protection, the answer their prescriber reaches for is a PPI such as omeprazole or lansoprazole, taken as directed. Taking naproxen with or just after food can also reduce irritation of the stomach lining, and is good practice especially when it is used occasionally. Whether you need acid protection, and which one, depends on your own risk factors, so it is a question for your GP or pharmacist rather than something to judge yourself.
Do you have to take omeprazole with naproxen?
Not everyone who takes naproxen needs omeprazole. It is generally recommended for people at higher risk of stomach problems, which is why some people are prescribed the two together and others are not. If you have been given both, keep taking them as prescribed. If you have been prescribed naproxen without any stomach protection and you are worried, that is worth raising with your pharmacist rather than deciding either way on your own.
Does omeprazole protect the whole gut?
Omeprazole is good at protecting the stomach, where the acid damage happens. It does not protect the small intestine in the same way, and there is evidence that reducing stomach acid can shift the balance of gut bacteria, which in some cases may even make naproxen's effects further down the gut more likely rather than less (Otani K, et al. (2017). Microbiota plays a key role in non-steroidal anti-inflammatory drug-induced small intestinal damage. Digestion. https://pubmed.ncbi.nlm.nih.gov/28052268/). This is not a reason to avoid omeprazole where it has been prescribed. It is a reason to look after the wider gut as well, which the rest of this guide covers.
Naproxen and the gut microbiome
While damage to the stomach lining is well known, research increasingly shows that NSAIDs also affect the gut microbiome, the community of bacteria, fungi and other microbes that plays a part in digestion, immunity, and inflammation.
NSAIDs like naproxen have been shown to:
- Alter which gut bacteria are present
- Reduce the variety of bacteria in the gut
- Disrupt the gut barrier, potentially contributing to a leaky gut
- Increase the chance of an imbalance between beneficial gut bacteria such as Bifidobacterium and less helpful bacteria
The mechanism is reasonably well described: once the gut lining is disrupted, bacterial products can trigger inflammation that keeps the cycle going (Otani K, et al. (2017), as above). This disruption can contribute to symptoms such as bloating, wind, reflux, and irregular bowel movements.
How to protect your gut when taking naproxen
If you take naproxen, especially over the long term, there are steps that may protect both your stomach lining and your wider gut. None of these replaces your medicine or any acid protection you have been prescribed.
A gut-friendly diet
Eating a diet rich in fibre and foods that are good for gut health helps support the gut barrier and a varied microbiome.
Include:
- Leafy greens (spinach, kale, rocket)
- Cruciferous vegetables (broccoli, cabbage, cauliflower)
- Whole grains (oats, quinoa)
- Fermented foods (kefir, sauerkraut, live yoghurt)
- Fibre-rich foods that feed gut bacteria (onions, garlic, leeks, asparagus)
- Polyphenol-rich foods (berries, olive oil, green tea)
Try to limit excessive alcohol, ultra-processed foods, and refined sugars, which can add to inflammation and imbalance.
If you also take a PPI, know the trade-offs
PPIs such as omeprazole are effective at protecting the stomach when you take an NSAID, and where one has been prescribed you should keep taking it. It is worth knowing that long courses of PPIs carry their own considerations for the gut, including a moderately higher chance of small intestinal bacterial overgrowth (Su T, et al. (2018). Meta-analysis: proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth. Journal of Gastroenterology. https://pubmed.ncbi.nlm.nih.gov/28770351/) and a small, dose-related increase in the risk of gut infections such as C. difficile (Finke M, et al. (2025). Proton pump inhibitors and the risk of Clostridioides difficile infection: a systematic review and dose-response meta-analysis. Journal of Infection. https://pubmed.ncbi.nlm.nih.gov/40239816/). This is background for a conversation with your pharmacist about using the lowest effective dose for the time you need it, not a reason to stop.
Live cultures
Some research suggests that live-culture supplements may help reduce NSAID-related gut irritation by supporting the gut lining and competing with less helpful bacteria. Species such as Lactobacillus rhamnosus and Bifidobacterium longum have been studied, but results vary between people and the evidence is still developing, so treat this as something that may help rather than a proven remedy. If you take other medicines, check with your pharmacist before starting a supplement.
Take naproxen with food
Taking naproxen with or just after a meal can reduce irritation of the stomach lining and acid exposure. This remains sensible practice, especially with occasional use.
Which painkiller is best for your stomach?
Taken regularly or at higher strengths, most NSAIDs can irritate the stomach or cause ulcers, and they can also influence the make-up of the gut microbiome, which can lead to an imbalance in gut bacteria, known as dysbiosis. Which painkiller suits you depends on your health, other medicines, and why you need pain relief, so it is a decision to make with your GP or pharmacist rather than from a general article.
As a rule of thumb, paracetamol is gentler on the stomach than NSAIDs and is often suggested first for mild pain, though it is not suitable or effective for every problem. Some NSAIDs, such as ibuprofen, also come as gels applied to the skin, which act more locally. If you have a long-term condition that means you need regular pain relief, ask your pharmacist which option is the best fit for you.
When to speak to your GP or pharmacist
Speak to a pharmacist or GP if naproxen is giving you ongoing indigestion, stomach discomfort, or changes in bowel habit, or if you want to review whether you need acid protection alongside it.
Some symptoms need prompt medical attention rather than diet changes or testing. Seek advice straight away if you have any of the following:
- Blood in your stool, or black, tarry stools
- Vomiting blood, or vomit that looks like coffee grounds
- Severe or persistent stomach pain
- Unexplained weight loss
- A persistent change in bowel habit lasting more than three weeks
- Difficulty swallowing
These can have many causes, but any of them should be checked by a clinician rather than managed at home.
Understanding your own gut
Because NSAIDs and acid-reducing medicines affect people differently, a broad picture of your own gut bacteria can be more useful than general advice. A gut microbiome test that measures a wide range of gut bacteria can show whether your own balance looks disrupted, which can then guide diet changes with your GP or pharmacist. It may help identify an imbalance or low diversity. It does not diagnose any condition and is not a substitute for medical care.
Sources
- Drini M (2017). Peptic ulcer disease and non-steroidal anti-inflammatory drugs. Australian Prescriber. https://pubmed.ncbi.nlm.nih.gov/28798512/
- Otani K, et al. (2017). Microbiota plays a key role in non-steroidal anti-inflammatory drug-induced small intestinal damage. Digestion. https://pubmed.ncbi.nlm.nih.gov/28052268/
- Su T, et al. (2018). Meta-analysis: proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth. Journal of Gastroenterology. https://pubmed.ncbi.nlm.nih.gov/28770351/
- Finke M, et al. (2025). Proton pump inhibitors and the risk of Clostridioides difficile infection: a systematic review and dose-response meta-analysis. Journal of Infection. https://pubmed.ncbi.nlm.nih.gov/40239816/
