A presumptive diagnosis of fungal keratitis requires immediate empirical therapy. Natamycin ophthalmic suspension is the drug of choice for filamentous fungal infection. Fluconazole ophthalmic solution is recommended for Candida infection of the cornea. Amphotericin B eye drops may be required for non-responding cases, but can be quite toxic and requires expert pharmacist for preparation. Other medications have also been tried with moderate success. Consult your eye care professional in any case as they will have the best treatment.

The infection typically takes a long time to heal, since the fungus itself is slow growing. Corneal perforation can occur in patients with untreated or partially treated infectious keratitis and requires surgical intervention in the form of corneal transplantation.

Antifungal drugs are used to treat mycoses. Depending on the nature of the infection, a topical or systemic agent may be used.

Example of antifungals include: fluconazole which is the basis of many over-the-counter antifungal treatments. Another example is amphotericin B which is more potent and used in the treatment of the most severe fungal infections that show resistance to other forms of treatment and it is administered intravenously.

Drugs to treat skin infections are the azoles: ketoconazole, itraconazole, terbinafine among others.

Yeast infections in the vagina, caused by "Candida albicans", can be treated with medicated suppositories such as tioconazole and pessaries whereas skin yeast infections are treated with medicated ointments.

Keeping the skin clean and dry, as well as maintaining good hygiene, will help larger topical mycoses. Because fungal infections are contagious, it is important to wash after touching other people or animals. Sports clothing should also be washed after use.

When no pus is present, warm soaks for acute paronychia is reasonable, even though there is a lack of evidence to support its use. Antibiotics such as clindamycin or cephalexin are also often used, the first being more effective in areas where MRSA is common. If there are signs of an abscess (the presence of pus) drainage is recommended.

Chronic paronychia is treated by avoiding whatever is causing it, a topical antifungal, and a topical steroid. In those who do not improve following these measures oral antifungals and steroids may be used or the nail fold may be removed surgically.

For the allergic type, cool water poured over the face with the head inclined downward constricts capillaries, and artificial tears sometimes relieve discomfort in mild cases. In more severe cases, nonsteroidal anti-inflammatory medications and antihistamines may be prescribed. Persistent allergic conjunctivitis may also require topical steroid drops.

Viral conjunctivitis usually resolves on its own and does not require any specific treatment. Antihistamines (e.g., diphenhydramine) or mast cell stabilizers (e.g., cromolyn) may be used to help with the symptoms. Povidone iodine has been suggested as a treatment, but as of 2008 evidence to support it was poor.

Most treatments are topical or oral antifungal medications.

Topical agents include ciclopirox nail paint, amorolfine or efinaconazole. Some topical treatments need to be applied daily for prolonged periods (at least 1 year). Topical amorolfine is applied weekly. Topical ciclopirox results in a cure in 6% to 9% of cases; amorolfine might be more effective. Ciclopirox when used with terbinafine appears to be better than either agent alone.

Oral medications include terbinafine (76% effective), itraconazole (60% effective) and fluconazole (48% effective). They share characteristics that enhance their effectiveness: prompt penetration of the nail and nail bed, persistence in the nail for months after discontinuation of therapy. Ketoconazole by mouth is not recommended due to side effects. Oral terbinafine is better tolerated than itraconazole. For superficial white onychomycosis, systemic rather than topical antifungal therapy is advised.

Otomycosis is treated by debridment followed with topical azole antifungals, and symptomatically managed with oral antihistamines. Per a study in Iran 10cc acetic acid 2% plus 90 cc of isopropyl alcohol 70% was effective.

If mucormycosis is suspected, amphotericin B therapy should be immediately administered due to the rapid spread and high mortality rate of the disease. Amphotericin B is usually administered for an additional 4–6 weeks after initial therapy begins to ensure eradication of the infection. Isavuconazole was recently FDA approved to treat invasive aspergillosis and invasive mucormycosis.

After administration of either amphotericin B or posaconazole, surgical removal of the "fungus ball" is indicated. The disease must be monitored carefully for any signs of reemergence.

Surgical therapy can be very drastic, and in some cases of disease involving the nasal cavity and the brain, removal of infected brain tissue may be required. In some cases surgery may be disfiguring because it may involve removal of the palate, nasal cavity, or eye structures. Surgery may be extended to more than one operation. It has been hypothesized that hyperbaric oxygen may be beneficial as an adjunctive therapy because higher oxygen pressure increases the ability of neutrophils to kill the organism.

Chemical (keratolytic) or surgical debridement of the affected nail appears to improve outcomes.

As of 2014 evidence for laser treatment is unclear as the evidence is of low quality and varies by type of laser.

As of 2013 tea tree oil has failed to demonstrate benefit in the treatment of onychomycosis. A 2012 review by the National Institutes of Health found some small and tentative studies on its use.

Chromoblastomycosis is very difficult to cure. The primary treatments of choice are:

- Itraconazole, an antifungal azole, is given orally, with or without flucytosine.

- Alternatively, cryosurgery with liquid nitrogen has also been shown to be effective.

Other treatment options are the antifungal drug terbinafine, an experimental drug posaconazole, and heat therapy.

Antibiotics may be used to treat bacterial superinfections.

Amphotericin B has also been used.

Oral Antibiotics: Ophthalmologists or optometrists may prescribe a low-dose, oral antibiotic such as Doxycycline.

Topical Antibiotics: If prescribed, topical creams or ointments can be applied after the cleansing of the lid margin. A small amount of antibiotic ophthalmic ointment is spread along the lid fissure with a swab or fingertip, while the eyes are closed. It is prescribed for use prior to bedtime to avoid blurred vision. Another method to reduce side effects of blepharitis are antibiotics such as erythromycin or sulfacetamide, which are used via eye drops, creams, or ointments on the eyelid margin. blepharitis caused by Demodex mites can be treated using a diluted solution of tea tree oil, via application by a cotton swab, for 5–10 minutes per day.

Steroid eyedrops/ointments: Eye drops or ointments containing corticosteroids are frequently used in conjunction with antibiotics and can reduce eyelid inflammation.

In bovines, an infestation is difficult to cure, as systemic treatment is uneconomical. Local treatment with iodine compounds is time-consuming, as it needs scraping of crusty lesions. Moreover, it must be carefully conducted using gloves, lest the worker become infested.

Fungal meningitis is treated with long courses of high dose antifungal medications. The duration of treatment is dependent upon the causal pathogen and the patient's ability to stave off the infection; for patients with a weaker immune system or diabetes, treatment will often take longer.

The treatment of Majocchi's disease can be difficult because the condition can slowly progress and is chronic in nature. After a period of time, the lesions can reoccur. Even though the condition has improved, there is always the possibility of reoccurrence. There are treatments available to help improve the symptoms, however, there is no absolute cure for the disease. Some of these treatments include the application of topical steroids and lotions and ultraviolet therapy. The use of narrowband UVB and psoralen plus UVA have shown to be effective treatments for some patients with pigmented purpuric dermatoses. Majocchi granuloma also commonly occurs as a result of the use of potent topical steroids on unsuspected tinea. Historically, antifungal therapy has been successful in controlling MG in most instances. Therapies that have been used, included oral potassium iodide, mildly filtered local X-radiation, and topical applications of Asterol as a fungicide in both tincture and ointment forms. In modern medicine, systemic antifungals, such as griseofulvin, ketoconazole, and itraconazole, are the pillars of therapy, as they are safe and effective. The duration of therapy should be at least 4–8 weeks, and treatment should be continued until all lesions are cleared. Currently, no data about relapse rates or the complications of not treating Majocchi granuloma exist.

Treatment for fungal sinusitis can include surgical debridement; helps by slowing progression of disease thus allowing time for recovery additionally we see the options below:

- In the case of invasive fungal sinusitis, echinocandins, voriconazole, and amphoterecin (via IV) may be used

- For allergic fungal sinusitis, systemic corticosteroids like prednisolone, methylprednisolone are added for their anti-inflammatory effect, bronchodilators and expectorants help to clear secretions in the sinuses.

Treatment options in persons without HIV-infection have not been well studied. Intravenous Amphotericin B combined with flucytosine by mouth is recommended.

Persons living with AIDS often have a greater burden of disease and higher mortality (30-70% at 10-weeks), but recommended therapy is with amphotericin B and flucytosine. Where flucytosine is not available (many low and middle income countries), fluconazole should be used with amphotericin. Amphotericin-based induction therapy has much greater microbiologic activity than fluconazole monotherapy with 30% better survival at 10-weeks. Based on a systematic review of existing data, the most cost-effective induction treatment in resource-limited settings appears to be one week of amphotericin B coupled with high-dose fluconazole. After initial induction treatment as above, typical consolidation therapy is with oral fluconazole for at least 8 weeks used with secondary prophylaxis with fluconazole thereafter.

The decision on when to start treatment for HIV appears to be very different than other opportunistic infections. A large multi-site trial supports deferring ART for 4–6 weeks was overall preferable with 15% better 1-year survival than earlier ART initiation at 1–2 weeks after diagnosis. A Cochrane review also supports the delayed starting of treatment until cryptococcosis starts improving with antifungal treatment.

There are many topical antifungal drugs useful in the treatment of athlete's foot including: miconazole nitrate, clotrimazole, tolnaftate (a synthetic thiocarbamate), terbinafine hydrochloride, butenafine hydrochloride and undecylenic acid. The fungal infection may be treated with topical antifungal agents, which can take the form of a spray, powder, cream, or gel. Topical application of an antifungal cream such as terbinafine once daily for one week or butenafine once daily for two weeks is effective in most cases of athlete's foot and is more effective than application of miconazole or clotrimazole. Plantar-type athlete's foot is more resistant to topical treatments due to the presence of thickened hyperkeratotic skin on the sole of the foot. Keratolytic and humectant medications such as urea, salicyclic acid (Whitfield's ointment), and lactic acid are useful adjunct medications and improve penetration of antifungal agents into the thickened skin. Topical glucocorticoids are sometimes prescribed to alleviate inflammation and itching associated with the infection.

A solution of 1% potassium permanganate dissolved in hot water is an alternative to antifungal drugs. Potassium permanganate is a salt and a strong oxidizing agent.

Treatment requires both systemic oral treatment with most of the same drugs used in humans—terbinafine, fluconazole, or itraconazole—as well as a topical "dip" therapy.

Because of the usually longer hair shafts in pets compared to those of humans, the area of infection and possibly all of the longer hair of the pet must be clipped to decrease the load of fungal spores clinging to the pet's hair shafts. However, close shaving is usually not done because nicking the skin facilitates further skin infection.

Twice-weekly bathing of the pet with diluted lime sulfur dip solution is effective in eradicating fungal spores. This must continue for 3 to 8 weeks.

Washing of household hard surfaces with 1:10 household sodium hypochlorite bleach solution is effective in killing spores, but it is too irritating to be used directly on hair and skin.

Pet hair must be rigorously removed from all household surfaces, and then the vacuum cleaner bag, and perhaps even the vacuum cleaner itself, discarded when this has been done repeatedly. Removal of all hair is important, since spores may survive 12 months or even as long as two years on hair clinging to surfaces.

Warm Compresses: "Soften lid margin debris and oils" by placing a very warm wet compress such as a clean, warm, wet washcloth over the closed eyelids for five minutes. Re-wet and reapply it as it cools. This warms, softens, and loosens crusty and oily eyelid gland deposits.

Eyelid Hygiene: "Remove lid margin debris" immediately after the warm compresses by gently washing the eyelids with a warm, wet, soapy washcloth to remove accumulated debris. Use a diluted, hypoallergenic baby shampoo. Gently rub along the lid margins, keeping the eyes shut. Too much soap or shampoo may remove the essential oil layer of the eyes' tear film and create further stress to the eye, as well as dry eye discomfort. A moist cotton swab soaked in a cup of water and baby shampoo may be used to rub along the lid margins while tilting the lid outward with the other hand to avoid this problem. Finally, rinse the eyelid with warm water and gently dry with a towel. "Eye make-up" should not be used while inflammation is present. "Dandruff shampoo" can be helpful if dandruff is contributing to blepharitis and may relieve blepharitis symptoms.

Drugs like ketoconazole,

voriconazole, and itraconazole are generally employed in treating the infection. Actinomycetes usually respond well to medical treatment, but the eumycetes are generally resistant and may require surgical interventions including amputation.

No vaccine is available. Simple hygienic precautions like wearing shoes or sandals while working in fields, and washing hands and feet at regular intervals may help prevent the disease.

The treatment of choice by dermatologists is a safe and inexpensive oral medication, griseofulvin, a secondary metabolite of the fungus "Penicillium griseofulvin". This compound is "fungistatic" (inhibiting the growth or reproduction of fungi) and works by affecting the microtubular system of fungi, interfering with the mitotic spindle and cytoplasmic microtubules. The recommended pediatric dosage is 10 mg/kg/day for 6–8 weeks, although this may be increased to 20 mg/kg/d for those infected by "T. tonsurans", or those who fail to respond to the initial 6 weeks of treatment. Unlike other fungal skin infections that may be treated with topical therapies like creams applied directly to the afflicted area, griseofulvin must be taken orally to be effective; this allows the drug to penetrate the hair shaft where the fungus lives. The effective therapy rate of this treatment is generally high, in the range of 88–100%.

Other oral antifungal treatments for tinea capitis also frequently reported in the literature include terbinafine, itraconazole, and fluconazole; these drugs have the advantage of shorter treatment durations than griseofulvin. However, concern has been raised about the possibility of rare side effects like liver toxicity or interactions with other drugs; furthermore, the newer drug treatments tend to be more expensive than griseofulvin.

On September 28, 2007, the U.S. Food and Drug Administration stated that Lamisil (Terbinafine hydrochloride, by Novartis AG) is a new treatment approved for use by children aged 4 years and older. The antifungal can be sprinkled on a child's food to treat the infection. Lamisil carries hepatotoxic risk, and can cause a metallic taste in the mouth.

Tinea cruris is best treated with topical antifungal medications of the allylamine or azole type. The evidence is best for terbinafine and naftifine but other agents may also work.

The benefits of the use of topical steroids in addition to an antifungal is unclear. There might be a greater cure rate but no guidelines currently recommend its addition. The effect of Whitfield's ointment is also unclear.