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.

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.

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.

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.

Sulfonamides are the traditional remedies to paracoccidiodomycosis. They were introduced by Oliveira Ribeiro and used for more than 50 years with good results. The most-used sulfa drugs in this infection are sulfadimethoxime, sulfadiazine, and co-trimoxazole. This treatment is generally safe, but several adverse effects can appear, the most severe of which are the Stevens-Johnson syndrome and agranulocytosis. Similarly to tuberculosis treatment, it must be continued for up to three years to eradicate the fungus, and relapse and treatment failures are not unusual.

Antifungal drugs such as amphotericin B or itraconazole and ketoconazole are more effective in clearing the infection, but are limited by their cost when compared with sulfonamides.During therapy, fibrosis can appear and surgery may be needed to correct this. Another possible complication is Addisonian crisis. The mortality rate in children is around 7-10%.

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.

Most cases are treated by application of topical antifungal creams to the skin, but in extensive or difficult to treat cases systemic treatment with oral medication may be required. The over-the-counter options include tolnaftate.

Among the available prescription drugs, the evidence is best for terbinafine and naftifine, but other agents may also work.

Topical antifungals are applied to the lesion twice a day for at least 3 weeks. The lesion usually resolves within 2 weeks, but therapy should be continued for another week to ensure the fungus is completely eradicated. If there are several ringworm lesions, the lesions are extensive, complications such as secondary infection exist, or the patient is immunocompromised, oral antifungal medications can be used. Oral medications are taken once a day for 7 days and result in higher clinical cure rates. The antifungal medications most commonly used are itraconazole and terbinafine.

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.

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.

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.

Enrofloxacin and trimethoprim potentiated sulfonamides are amongst the antibiotics commonly prescribed by veterinarians to treat severe bacterial infection of the pastern. Systemic antifungal therapy is rarely necessary, but ketoconazole, itraconazole, and fluconazole are sometimes recommended with variable success.

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.

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.

Good success has been noted by some with topical steroids such as triamcinolone and betamethasone applied to the lesions in conjunction with other treatments containing Kunzea.

For severe or refractory cases of athlete's foot oral terbinafine is more effective than griseofulvin. Fluconazole or itraconazole may also be taken orally for severe athlete's foot infections. The most commonly reported adverse effect from these medications is gastrointestinal upset.

Treatment of sporotrichosis depends on the severity and location of the disease. The following are treatment options for this condition:

- Saturated potassium iodide solution

- Itraconazole (Sporanox) and fluconazole

- Amphotericin B

- Terbinafine

- Newer triazoles

- Surgery

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.

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.

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.

The exact cause of Majocchi's granuloma is not well established however a dysfunctinoal immune system may be a causative factor. The first form of MG, the superficial perifollicular form occurs predominately on the legs of otherwise healthy young women who repeatedly shave their legs and develop hair follicle occlusions that directly or indirectly disrupt the follicle and allow for passive introduction of the organism into the dermis. Hence, the physical barrier of the skin is important because it prevents the penetration of microorganisms. Physical factors that play a major role in inhibiting dermal invasion include the interaction among keratin production, the rate of epidermal turnover, the degree of hydration and lipid composition of the stratum corneum, CO levels, and the presence or absence of hair. Keratin and/or necrotic material can also be introduced into the dermis with an infectious organism to further enhance the problem. In immunocompromised individuals, the use of topical corticosteroids may lead to a dermatophyte infection due to local immunosuppression.

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.

Medical professionals recommend a preventative based approach of stopping fungus before it occurs. Prevention is preferable over a reactive treatment approach. The preventative based approach involves removing heat and moisture to the groin area.

- Dry off with a clean towel immediately after showering, swimming or perspiring.

- Shower after physical activities.

- Wear underwear with high air and moisture permeability fabric, such as linen (flax).

Because fungi prefer warm, moist environments, preventing ringworm involves keeping skin dry and avoiding contact with infectious material. Basic prevention measures include:

- Washing hands after handling animals, soil, and plants.

- Avoiding touching characteristic lesions on other people.

- Wearing loose-fitting clothing.

- Practicing good hygiene when participating in sports that involve physical contact with other people.

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.