When You Can't Get Natamycin: What Are Your Options?

A fungal eye infection is stressful enough without the added frustration of not being able to find your medication. If your doctor prescribed Natamycin (brand name Natacyn) and you're struggling to locate it at a pharmacy, you may be wondering: are there alternatives?

The short answer is yes — there are other antifungal medications that can treat fungal eye infections. However, they come with important differences you should understand. In this post, we'll explain what Natamycin is, how it works, and walk through the most common alternatives your doctor may consider.

What Is Natamycin?

Natamycin is a polyene antifungal medication available as a 5% ophthalmic suspension under the brand name Natacyn, manufactured by Alcon Laboratories. It is the only FDA-approved topical antifungal eye drop in the United States.

It's prescribed for fungal infections of the eye, including:

• Fungal keratitis — infection of the cornea, often caused by Fusarium or Aspergillus species
• Fungal conjunctivitis — infection of the membrane lining the eye
• Fungal blepharitis — infection of the eyelids

For a full overview of this medication, see our guide: What is Natamycin? Uses, dosage, and what you need to know.

How Does Natamycin Work?

Natamycin works by binding to ergosterol, a key component of fungal cell membranes. When Natamycin binds to ergosterol, it creates pores in the membrane, causing essential contents to leak out of the fungal cell. This process kills the fungus — making Natamycin fungicidal rather than just fungistatic.

Natamycin is particularly effective against filamentous fungi like Fusarium, which is the most common cause of fungal keratitis in many parts of the world. It also works against Candida, Aspergillus, Cephalosporium, and Penicillium species.

Learn more in our detailed post on how Natamycin works.

Why Might You Need an Alternative?

There are several reasons you might need a substitute for Natamycin:

• Pharmacy doesn't have it in stock — Natamycin is a specialty medication that most pharmacies don't routinely carry
• Cost is prohibitive — at $250 to $600 per bottle, not everyone can afford it, especially without insurance
• Supply disruption — as a single-source product, manufacturing issues can cause temporary shortages
• Your infection doesn't respond — some fungal species may be resistant, requiring a different antifungal

If your issue is simply finding a pharmacy with stock, we recommend trying Medfinder first — it can often locate Natamycin at pharmacies near you. But if the medication truly isn't available, the alternatives below may help.

Alternative 1: Voriconazole 1% Eye Drops (Compounded)

Voriconazole is a triazole antifungal that has become one of the most widely used alternatives to Natamycin for fungal keratitis. It works by inhibiting a fungal enzyme called lanosterol 14-alpha demethylase, which is essential for making ergosterol. Without ergosterol, the fungal cell membrane breaks down.

Key facts about Voriconazole eye drops:

• Typically compounded as a 1% ophthalmic solution
• Effective against a broad range of fungi including Aspergillus, Candida, and Fusarium
• Better corneal penetration than Natamycin, making it useful for deeper infections
• Not FDA-approved for ophthalmic use — must be obtained from a compounding pharmacy
• May cost $50 to $150 when compounded, depending on the pharmacy

Clinical studies have shown that Voriconazole can be as effective as Natamycin for certain types of fungal keratitis, particularly those caused by Aspergillus. However, for Fusarium keratitis, Natamycin has generally shown better results in head-to-head trials.

Alternative 2: Amphotericin B 0.15-0.5% Eye Drops (Compounded)

Amphotericin B is another polyene antifungal — the same drug class as Natamycin. It works through a similar mechanism: binding to ergosterol in the fungal cell membrane and disrupting its integrity.

Key facts about Amphotericin B eye drops:

• Compounded as a 0.15% to 0.5% ophthalmic solution
• Effective against Candida and Aspergillus
• Less effective than Natamycin against Fusarium
• Can cause more local eye irritation than Natamycin
• Not FDA-approved for ophthalmic use — requires a compounding pharmacy
• Cost varies but typically $40 to $120 when compounded

Amphotericin B is often used when Natamycin is unavailable or as an add-on therapy for severe infections. Because it shares a similar mechanism with Natamycin, it can be a reasonable substitute in many cases.

Alternative 3: Fluconazole 0.2% Eye Drops (Compounded)

Fluconazole is a triazole antifungal that is well-known in its oral form (brand name Diflucan). When compounded as eye drops, it can be used for fungal eye infections, particularly those caused by Candida species.

Key facts about Fluconazole eye drops:

• Compounded as a 0.2% ophthalmic solution
• Best suited for Candida keratitis
• Less effective against filamentous fungi like Fusarium and Aspergillus
• Good corneal penetration
• Generally well tolerated with minimal irritation
• Cost is typically $30 to $80 when compounded

Alternative 4: Oral Antifungal Therapy (Adjunct)

For severe or deep fungal eye infections, your ophthalmologist may add an oral antifungal medication to your treatment regimen. These are not replacements for topical therapy but can provide additional systemic antifungal coverage:

• Oral Voriconazole — commonly used for serious fungal keratitis, especially when there's a risk of deeper penetration
• Oral Itraconazole — another option for adjunct systemic therapy
• Oral Fluconazole — sometimes used for Candida-related eye infections

Oral antifungals have more potential for side effects and drug interactions than topical eye drops. Your doctor will weigh the risks and benefits carefully. For more on interactions, see our post on Natamycin drug interactions.

Important: Don't Switch Medications on Your Own

While it's helpful to know what alternatives exist, never switch or stop antifungal treatment without talking to your ophthalmologist. Fungal eye infections can worsen rapidly, and the wrong medication choice can lead to vision loss. Your doctor will choose an alternative based on:

• The specific type of fungus causing your infection (identified through lab cultures)
• The severity and depth of the infection
• Your response to current treatment
• Drug availability and cost

Final Thoughts

Natamycin is the gold standard for treating fungal eye infections, and for good reason — it has the broadest antifungal spectrum of any FDA-approved ophthalmic antifungal. But when you can't get it, alternatives like compounded Voriconazole, Amphotericin B, and Fluconazole can provide effective treatment for many patients.

Before exploring alternatives, try using Medfinder to locate Natamycin at pharmacies near you. And always work closely with your ophthalmologist to make sure you're getting the right treatment for your specific infection.