Using Fluconazole for Candida Overgrowth (Safety, Precautions & More)

Using Fluconazole for Candida Overgrowth (Safety, Precautions & More)

Candida overgrowth is a condition which affects many patients, especially those with existing gut problems and those with thyroid disease

Among the many treatments available are some which require a doctors prescription. 

In this article, we are going to focus on fluconazole (also known as Diflucan) which is a prescription medication which is particularly effective at killing the candida species. 

This medication is a potentially great option for many people because it is effective and does not typically carry negative side effects.


Candida Overgrowth & Treatment

Candida overgrowth, sometimes referred to as small intestinal fungal overgrowth or SIFO, is a condition characterized by an overgrowth of this fungus in your intestinal tract. 

The overgrowth of this fungus can lead to certain symptoms including fatigue (1), sinus infections (2), digestive issues (3), reduced absorption of nutrients (4), and food intolerance. 

There's obviously some controversy surrounding this condition which is apparent with some simple searches on the internet:

candida search results on google

This controversy stems from the fact that conventional medicine believes that candida is really only a serious issue if you are severely immunocompromised. 

Meanwhile, the integrative/natural community believes that candida is a common condition found in the intestinal tract of many people and which causes negative symptoms. 

The truth, as always, is really somewhere in between. 

My personal opinion is that candida overgrowth can certainly be an issue for some people while others may have the same level of fungus in their intestinal tract and not have any issues. 

Your susceptibility to candida and its effects probably has a lot to do with your own personal genetics (5), your personal history, your immune status, your gut status, and so on. 

But that's a topic for another day: 

I'm not going to get into the controversy surrounding this medical condition in this article but I at least want to point out that it exists. 

I'm going to assume, for now, that you know or at least suspect that you have this condition and you are looking for treatment. 

And the treatment we are going to focus on today is the prescription medication known as fluconazole. 

*Note: this isn't the only way to treat candida, though! Later we are going to discuss some natural options as well. 

What is Fluconazole? 

Fluconazole is a prescription medication, which means you need a doctor to give it to you, and it's designed to eradicate certain fungi. 

Fluconazole is typically given to people who have the manifestation of candida such as thrush or yeast infections. 

The good news is that it can also be used to treat intestinal candida/fungus as well. 

fluconazole chemical structure

And, if you are someone who has or who semi-frequently suffers from conditions such as thrush or vaginal yeast infections then there is a very high probability you also have candida in your intestinal tract. 

After all, where do you think the infections are coming from? 

Back to fluconazole for a minute. 

Fluconazole works by preventing certain fungi from keeping their cytoplasmic membrane intact. 

Basically, it helps weaken the 'shield' that protects fungus from outside forces. 

It has shown activity (meaning it can kill) the following species:

  • Candida albicans
  • Candida glabrata
  • Candida parapsilosis
  • Candida tropicalis
  • Cryptococcus neoformans

Some species, such as Candida krusei are considered to be resistant to fluconazole and so should not be used to treat that specific strain. 

Fluconazole is the generic medication while Diflucan is the name-brand. So either of these medications should work if you are attempting to treat your candida overgrowth. 

Fungal Resistance to Fluconazole

One potential downside to using fluconazole is the fact that many species of candida have become resistant to its effects. 

This concept also occurs with certain bacteria which have become antibiotic-resistant due to overuse of certain antibiotics. 

The same thing has occurred, at least somewhat, with fluconazole and candida (6). 

Certain species of candida have become resistant to fluconazole. 

As a patient, this is very important to know and understand. 


Because it may impact how you feel when you start taking fluconazole. 

Imagine you are taking fluconazole for candida but you aren't feeling any better while taking it. 

If this occurs, and you are sure your symptoms are at least mostly related to candida, it could be a tip-off that your species is resistant to fluconazole and that you may need a different type of therapy. 

Resistance to fluconazole seems to occur on a personal level. 

Meaning, the more times YOU use Diflucan or fluconazole the more resistant the strain of candida in YOUR body becomes (assuming it is not all killed off). 

So even though certain species of candida are resistant to fungal medications does not mean or guarantee that the species in your body will be resistant to them. 

Because of this, it's still worthwhile to try these medications (assuming you don't have any contraindications to using the medication). 

Side Effects

A couple points to remember as we talk about side effects of prescription medications. 

#1. Side effects always sound scary. 

Prescription medications must include ALL potential side effects which have ever been reported (even once and even if they were only closely associated but not caused directly by the medication). 

Have a healthy respect for side effects from medications but don't automatically assume that they will occur. 

#2. Side effects tend to be related to the DURATION of therapy and the DOSAGE you are using. 

Side effects caused by medications are typically dose-related. 

The higher the dose you are taking and the longer you are taking them the more likely you are to experience negative side effects. 

Fluconazole, for instance, is generally only used for a few days (sometimes up to a month), and at this level of usage, the risk for side effects is quite low. 

#3. Just because you CAN get these symptoms does not mean that you will.

The list of side effects is a list of all possible side effects but the risk that you will have any side effects is actually fairly low and in your favor. 

Major side effects are quite rare with most medications (if they weren't then the medication would be pulled from the market).

Common side effects typically fade on their own with time. 

I'm not necessarily advocating the use of fluconazole to treat Candida but I also want to be fair to the therapy. 

It's easy to jump on the back of prescriptions and convince yourself that they are always bad because of their potential for negative side effects. 

But the reason we know so much about these medications is that the FDA helps keep track of them. 

Nothing like that exists for dietary supplements (at least not to the same degree), so supplements probably CAN cause a variety of symptoms as well but no one is keeping track of them. 

Common side effects may include:

  • Nausea
  • Abdominal pain
  • Diarrhea
  • Rash
  • Vomiting

My experience has been that most people do not experience any negative side effects when taking fluconazole. 

Those who do have symptoms usually have a mild headache or an upset stomach which fades over the course of 5-7 days or so. 

More serious (but less common) side effects include:

  • QT prolongation
  • Anaphylactic reactions
  • Cholestasis
  • Liver failure/liver issues
  • Jaundice

*Note: I have never seen anyone react with any of these side effects and I have used this medication probably several hundred times. It doesn't mean that they don't occur but they are not common. 

You'll notice that many of these serious side effects have to do with the liver. 

Because of this, fluconazole should NOT be used in people who have known liver dysfunction. 

It should also NOT be used if you have a known hypersensitivity to fluconazole or to other 'azoles'. 

*Note: this is not a complete list of side effects of fluconazole. I just wanted you to be aware of SOME of the more common and more serious side effects potentially associated with this medication. 

For a more complete list of side effects, you can look here (7). 

Over the Counter Supplements vs Prescription Medications for Candida

It may be tempting to think or believe that prescription medications are always more powerful than over the counter supplements. 

And while this may make sense intuitively, it certainly isn't always the case. 

Some studies, such as this, have shown that herbal antibiotics/antifungals can be just as potent (if not more potent) than conventional prescription medications. 

Having said that, prescription medications certainly have their place, especially when treating gut-related issues such as SIFO (candida) and SIBO

If you prefer the 'all-natural' approach OR if you've tried Diflucan/fluconazole without success, there are still many options available to you. 

I've compiled a list of supplements below that you may want to consider if you have candida: 

  • Coconut oil (8) and/or monolaurin (9) - This over the counter food/fat has shown potent anti-fungal and anti-bacterial activity in some studies. 1-2 tablespoons per day may help kill off extra fungus in your GI tract. But be careful, don't go overboard on fat consumption or you may gain weight. You can also just get the monolaurin subfraction of coconut oil in this supplement
  • Essential oils (10) - Essential oils, when consumed, have both potent anti-bacterial and anti-fungal action. The key to getting them to work is using the right dose and getting them into your body. This may require carrier oils or encapsulation of the oils. 
  • Candibactin ar + br - For most cases, the combinations of these two supplements (Candibactin ar and candibactin br) is usually sufficient to kill off yeast overgrowth. This combination of essential oils (thyme, oregano, sage) and berberine is quite effective. This is probably because more diversity in antifungals equates to a higher kill rate of the fungus and a decreased resistance to whatever you are using. 
antimicrobial activity of coconut oil

These supplements can also be combined with prescription medications (such as fluconazole) to increase effectiveness and reduce the risk of fungal resistance. 

When I treat patients for fungal overgrowth or candida, I typically use multiple options for that very reason. 

Another important point to consider is that killing off candida is only part of the equation to treating your issue. 

If you kill off candida but do not fix the issues that caused it to overpopulate in the first place then you will eventually end up where you started. 

You will want to ensure that you take the proper precautions such as changing your diet (to avoid the foods that candida likes to eat and which make it grow), to reduce your stress (which can weaken your immune system), and provide your body with healthy probiotics to take the place of the candida once it's gone. 

These steps are all very important to not only treating candida but to also ensuring that it does NOT come back. 


Candida is incredibly common, though perhaps not quite as common as you may think, and should be addressed swiftly if identified. 

As a patient, you have MANY options for treatment available to you. 

Some available over the counter and some available via prescription only. 

Fluconazole/Diflucan falls into the last group and is an effective medication for treating candida in many cases (though not all). 

My recommendation is to use fluconazole in combination with other over the counter supplements to enhance its effectiveness. 

This combination of supplements should help you kill off fungal species in your gut (and other places) and diminish the likelihood that they will come back. 

Now I want to hear from you:

Are you suffering from candida overgrowth?

Do you suspect that you have it?

Have you used fluconazole before? Did it work for you? 

Why or why not?

Leave your questions or comments below! 

References (Click to Expand)

fluconazole yeast overgrowth

Dr. Westin Childs

About Dr. Westin Childs

Hey! I'm Westin Childs D.O. (former Osteopathic Physician). I don't practice medicine anymore and instead specialize in helping people like YOU who have thyroid problems, hormone imbalances, and weight loss resistance. I love to write and share what I've learned over the years. I also happen to formulate the best supplements on the market (well, at least in my opinion!) and I'm proud to say that over 45,000+ people have used them over the last 4.5 years. You can read more about my own personal health journey and why I am so passionate about what I do here.

26 thoughts on “Using Fluconazole for Candida Overgrowth (Safety, Precautions & More)”

  1. Hi Dr. Childs,

    Another very informative article. I do have a question you can perhaps help with? I have had low-grade candida overgrowth for many years, and a recent test showed IGG > 300. My doctor had me on a dose of oregano oil and caprylic acid which didn’t fully address the issue, and now I am on Berberine. My question is, have you seen any interaction between Berberine and LDN (I am on it for Hashimotos)? I started the Berberine (500 mg 2 times a day) a few days ago and I am experiencing muscle pain and a complete loss of appetite. I literally cannot eat more than one meal per day. I had a normal appetite before and ate roughly 1800 – 2200 calories which is now cut in half or more. My doctor seems to think it will normalize and taking care of the candida is more important, I am worried I will mess up my metabolism. FYI I am also on Armour Thyroid, Calcium D Glucarate and Glutathione supplements.

    Thank you!

  2. Thanks very much for this info, I have a high prob theory I have yeast/fungus/mold that has been causing intestinal problems in me for years and I don’t think I have ever tried this product though I have used the herbal things which haven’t stopped my decade long 24/7 diarrhea. I will combine it with all the herbals and coconut oil and see if I can make any headway against my issues.

  3. I have also had a low grade yeast infection for years. It mostly doesn’t bother me but I know it’s there. I have never had two diflucan pills in one treatment (3days apart). It did have an effect but only for a few days. For how long is it safe to take diflucan, what doses and how many days apart?

    • Hi Julie,

      It kind of depends on the person and the situation. But if you have yeast overgrowth, taking two pills of Diflucan is definitely not going to cut it.

  4. Hey Dr. Childs, can you comment on the dose and typical treatment duration for diflucan in regards to suspected candida gut overgrowth? Thank you.

  5. I feel certain I have candida issues, they just keep coming back. Fluconazole works for a bit, then right back to the same issues again. And I don’t digest foods completely. Constant sinusitis, tiredness, and inability to lose weight. I just got your Hypothyroid bundle and the Leptin Resistance Rx. I can tell a difference in how my energy and body feel already from 3 days of taking them, but I’m still tired and have some continuing signs of Candida. I feel like the Probiotics may need to be added for me to get the full results I’m looking for and to rebalance my gut. Any other suggestion? Or advice on the order I should be doing things?

    • Hi Elster,

      I would also work on a kill phase of botanicals/essential oils which are known to be anti-fungal. That combined with going sugar free for some time should be helpful (at least for the fungal overgrowth). This is just a starting point, though, as you may need much more than this.

      • Trying this now with the probiotics and a vegan diet, no sugars/alcohol/etc. Crossing the fingers! And thank you for the timely response! Will update after I receive everything and do this for a few weeks. : )

        • Okay, been going sugar free for almost 2 weeks, and I got my doctor to prescribe the Diflucan for 14 days. So, I’ll come back to report after the next 6 weeks or so to let you know what’s up… I’m feeling like this is going to work!! My energy is great, and I’m sleeping quite well!

          • Finished the Diflucan, now just continuing your diet and the supplements… I just keep losing weight, which is AWESOME!!! I’ll come back to report again after May 1st, my final day : )

  6. I have had an oral fungal infection for going on three months after a severe pneumonia in February and months on inhaled steroids. Immediately after stopping, my throat, esophagus and mouth became infected. A course of nystatin helped but did not get rid of it, then fluconazole which I stopped after a week because of no improvement. I tried combination of fluconazole and nystatin per my ND, and became very ill for several days. I then switched to natural approach using Biocidin and Olivirex. I also take NAC and coconut oil. But still the infection continues. After a return to the Ear nose and throat doctor, I was told to pick one of the anti fungals I was on and try it again!
    Another option given my was clotrimazole troches.
    I am concerned that I will simply strengthen the fungus/candida?
    by going back to the anti fungals I have used.
    I am at the end of my patience and hope.
    Any thoughts on what I can try now?
    Thanks for your article and any thoughts.

  7. I feel certain that I have Candida since I suffer constant sinus issues and have had problems with breath issues all my life. I am just completing my 3rd bundle of Hashimoto’s and have the weight loss bundle waiting as I have gained weight in my middle since the Hashimoto’s diagnosis. I am feeling better but have a ways ago. Advise please on the Candida issue.

    • Hi Sheila,

      Candida and SIBO (both gut conditions) tend to accompany many with Hashimoto’s/hypothyroidism so it is very possible.

  8. Hi Dr. Westin,

    Im Pete 27, have history of taking antibiotics and antacids (omeprazole and esomeprazole) and gaviscon for my acid reflux. I took FA and negative for parasites, but with results came with yeast in my stool. But I know yeast is normal in the gut as well.

    I’m pretty sure I have candida overgrowth in my gut, because of the presence of it in my stool that really looks like string cheese, and looks like cottage cheese when I have diarrhea, it usually causes diarrhea when I eat high sugar foods and take fruits like peach and papaya. I’m also noticing I might have oral thrush from the look of my tongue.

    I also have been on a diet of high whole grain and nuts and now I notice I usually have constipation for 1 or 2 days and have diarrhea on the 2nd or 3rd day.

    Now, I changed my diet to low sugar and as an Asian I cant remove my rice consumption, I also wonder if I should remove white rice in my diet..

    Anyway my doctor who is also my friend told me he is probably prescribing 100mg fluconazole but havent told me yet for how long since I havent seen him yet in person because of the covid situation.

    So my question is could you suggest any other diagnostics for me to get? and if you would prescribe me fluconazole whats the dosage and for how long…

  9. Hello,
    I suspect that both me and my two daughters, age 4 and 5, have Candidia growth issues in our gut. They have diarrhea type poos most often. I have had the same, as well as I’m getting weird headaches in the back of my head and neck most like pressure and slight itchy sensations. Could this be fungus? All my blood work came back normal including for hypothyroid so that’s why I wonder about yeast, fungus etc. What is a safe treatment for children to get rid of candidia? Thank you so much

  10. Hello I know this is an old article but I am hopeful you are still responding. I have been very ill for about a year with tons of testing and no answers recently had a compressive stool test that showed a +3 on candida parapilosis however my blood test came back negative. My doctor is willing to treat with fluconazole but I am nervous about die off as every time i have tried a natural herb like oregano or garlic by day 3 I feel very sick again which is scary because I do mot want to be bed ridden again. Most symptoms are GI but also night sweats, chills, and anxiety plus some hormonal stuff. Do you think it worth treating the candida with fluconazole and can Candida P. In the gut not show up in the blood?

  11. Hello doctor, I have candida for long time I never addressed properly! I am on a low carb diet but I am so fed up with it! I need quick solution. What is the quickest way!?
    I have constant oral thrush and bloat, pain in my intestines

    • Hi Diana,

      Unfortunately, there really isn’t a quick solution. It can sometimes be easy to treat but it really depends on the individual. Most treatments take time, dietary changes, supplements, probiotics, prebiotics, and enzymes.

  12. I had diverticulitis 5 times in one year and eventually led to a sigmoid resection. As a result of all the heavy duty antibiotics I was on for like a year, my gut has never been the same. I was taking Flagyl and Vanco. While all of those gut issues have been fixed, I am left with constant overgrowth from all of the damage. I am trying to find a cure for this once and for all. I have tried taking Diflucan, but probably am not taking enough to KILL off the abundant overgrowth. I started drinking and making my own KEFIR milk at home to try to replace the good flora in my gut and keep the yeast in check. I definitely notice a difference if I stop drinking the milk (ie: severe heartburn, bloating and bouts of constipation) What is your opinion of KEFIR? Is there some way to combine it with supplementation to finally rid myself of these symptoms?


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