Candidiasis is treated with antifungal medications; these include clotrimazole, nystatin, fluconazole, voriconazole, amphotericin B, and echinocandins. Intravenous fluconazole or an intravenous echinocandin such as caspofungin are commonly used to treat immunocompromised or critically ill individuals.

The 2016 revision of the clinical practice guideline for the management of candidiasis lists a large number of specific treatment regimens for "Candida" infections that involve different "Candida" species, forms of antifungal drug resistance, immune statuses, and infection localization and severity. Gastrointestinal candidiasis in immunocompetent individuals is treated with 100–200 mg fluconazole per day for 2–3 weeks.

Mouth and throat candidiasis are treated with antifungal medication. Oral candidiasis usually responds to topical treatments; otherwise, systemic antifungal medication may be needed for oral infections. Candidal skin infections in the skin folds (candidal intertrigo) typically respond well to topical antifungal treatments (e.g., nystatin or miconazole). Systemic treatment with antifungals by mouth is reserved for severe cases or if treatment with topical therapy is unsuccessful. Candida esophagitis may be treated orally or intravenously; for severe or azole-resistant esophageal candidiasis, treatment with amphotericin B may be necessary.

Vaginal yeast infections are typically treated with topical antifungal agents. A one-time dose of fluconazole is 90% effective in treating a vaginal yeast infection. For severe nonrecurring cases, several doses of fluconazole is recommended. Local treatment may include vaginal suppositories or medicated douches. Other types of yeast infections require different dosing. Gentian violet can be used for thrush in breastfeeding babies. "C. albicans" can develop resistance to fluconazole, this being more of an issue in those with HIV/AIDS who are often treated with multiple courses of fluconazole for recurrent oral infections.

For vaginal yeast infection in pregnancy, topical imidazole or triazole antifungals are considered the therapy of choice owing to available safety data. Systemic absorption of these topical formulations is minimal, posing little risk of transplacental transfer. In vaginal yeast infection in pregnancy, treatment with topical azole antifungals is recommended for 7 days instead of a shorter duration.

No benefit from probiotics has been found for active infections.

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.

The following treatments are typically recommended:

- Intravaginal agents: butoconazole, clotrimazole, miconazole, nystatin, tioconazole, terconazole. Candidal vulvovaginitis in pregnancy should be treated with intravaginal clotrimazole or nystatin for at least 7 days. All are more or less equally effective.

- By mouth: fluconazole as a single dose. For severe disease another dose after 3 days may be used.

Short-course topical formulations (i.e., single dose and regimens of 1–3 days) effectively treat uncomplicated candidal vulvovaginitis. The topically applied azole drugs are more effective than nystatin. Treatment with azoles results in relief of symptoms and negative cultures in 80–90% of patients who complete therapy.

The creams and suppositories in this regimen are oil-based and might weaken latex condoms and diaphragms. Treatment for vagina thrush using antifungal medication is ineffective in up to 20% of cases. Treatment for thrush is considered to have failed if the symptoms do not clear within 7–14 days. There are a number of reasons for treatment failure. For example, if the infection is a different kind, such as bacterial vaginosis (the most common cause of abnormal vaginal discharge), rather than thrush.

Antifungals are used for treatment with the specific type and dose depending on the patient's age, immune status, and specifics of the infection. For most adults, the initial treatment is an echinocandin class antifungal (caspofungin, micafungin, or anidulafungin) given intravenously. Fluconazole, amphotericin B, and other antifungals may also be used. Treatment normally continues for two weeks after resolution of signs and symptoms and "Candida" yeasts can no longer can be cultured from blood samples. Some forms of invasive candidiasis, such as infections in the bones, joints, heart, or central nervous system, usually need to be treated for a longer period. Retrospective observational studies suggest that prompt presumptive antifungal therapy (based on symptoms or biomarkers) is effective and can reduce mortality.

Up to 40% of women seek alternatives to treat vaginal yeast infection. Example products are herbal preparations, probiotics and vaginal acidifying agents. Other alternative treatment approaches include switching contraceptive, treatment of the sexual partner and gentian violet. However, the effectiveness of such treatments has not received much study.

Probiotics (either as pills or as yogurt) do not appear to decrease the rate of occurrence of vaginal yeast infections. No benefit has been found for active infections. Example probiotics purported to treat and prevent candida infections are Lactobacillus fermentum RC-14, Lactobacillus fermentum B-54, Lactobacillus rhamnosus GR-1, Lactobacillus rhamnosus GG and Lactobacillus acidophilus.

There is no evidence to support the use of special cleansing diets and colonic hydrotherapy for prevention.

Preventative antifungal treatment is supported by studies, but only for specific high-risk groups in intensive care units with conditions that put them at high risk for the disease. For example, one group would be patients recovering from abdominal surgery that may have gastrointestinal perforations or anastomotic leakage. Antifungal prophylaxis can reduce the incidence of fungemia by approximately 50%, but has not been shown to improve survival. A major challenge limiting the number of patients receiving prophylaxis to only those that can potentially benefit, thereby avoiding the creation of selective pressure that can lead to the emergence of resistance.

The current first-line treatment is fluconazole, 200 mg. on the first day, followed by daily dosing of 100 mg. for at least 21 days total. Treatment should continue for 14 days after relief of symptoms.

Other therapy options include:

- nystatin is not an effective treatment for esophageal candidiasis. It can be used as (swish, do not swallow) treatment for oral candidiasis that occurs with the use of asthma pumps.

- other oral triazoles, such as itraconazole

- caspofungin, used in refractory or systemic cases

- amphotericin, used in refractory or systemic cases

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.

Oral candidiasis can be treated with topical anti-fungal drugs, such as nystatin, miconazole, Gentian violet or amphotericin B.

Underlying immunosuppression may be medically manageable once it is identified, and this helps prevent recurrence of candidal infections.

Patients who are immunocompromised, either with HIV/AIDS or as a result of chemotherapy, may require systemic treatment with oral or intravenous administered anti-fungals.

If candidiasis is secondary to corticosteroid or antibiotic use, then use may be stopped, although this is not always a feasible option. Candidiasis secondary to the use of inhaled steroids may be treated by rinsing out the mouth with water after taking the steroid. Use of a spacer device to reduce the contact with the oral mucosa may greatly reduce the risk of oral candidiasis.

In recurrent oral candidiasis, the use of azole antifungals risks selection and enrichment of drug-resistant strains of candida organisms. Drug resistance is increasingly more common and presents a serious problem in persons who are immunocompromised.

Prophylactic use of antifungals is sometimes employed in persons with HIV disease, during radiotherapy, during immunosuppressive or prolonged antibiotic therapy as the development of candidal infection in these groups may be more serious.

The candidal load in the mouth can be reduced by improving oral hygiene measures, such as regular toothbrushing and use of anti-microbial mouthwashes. Since smoking is associated with many of forms of oral candidiasis, cessation may be beneficial.

Good denture hygiene involves regular cleaning of the dentures, and leaving them out of the mouth during sleep. This gives the mucosa a chance to recover, while wearing a denture during sleep is often likened to sleeping in one's shoes. In oral candidiasis, the dentures may act as a reservoir of Candida species, continually reinfecting the mucosa once antifungal medication is stopped. Therefore, they must be disinfected as part of the treatment for oral candidiasis. There are commercial denture cleaner preparations for this purpose, but it is readily accomplished by soaking the denture overnight in a 1:10 solution of sodium hypochlorite (Milton, or household bleach). Bleach may corrode metal components, so if the denture contains metal, soaking it twice daily in chlorhexidine solution can be carried out instead. An alternative method of disinfection is to use a 10% solution of acetic acid (vinegar) as an overnight soak, or to microwave the dentures in 200mL water for 3 minutes at 650 watts. Antifungal medication can also be applied to the fitting surface of the denture before it is put back in the mouth. Other problems with the dentures, such as inadequate occlusal vertical dimension may also need to be corrected in the case of angular cheilitis.

Neutropenic vs non-neutropenic candidemia is treated differently.

An intravenous echinocandin such as anidulafungin, caspofungin or micafungin is recommended as first-line therapy for fungemia, specifically candidemia. Oral or intravenous fluconazole is an acceptable alternative. The lipid formulation amphotericin B is a reasonable alternative if there is limited antifungal availability, antifungal resistance, or antifungal intolerance.

Geotrichosis generally has a good prognosis and patients generally have successful recovery. However, there is not a standard treatment for geotrichosis. There are several types of antimicrobial or antifungal compounds that can be used for geotrichosis treatment. One type of treatment of geotrichosis can involve miconazole and ketoconazole, which has shown to improve cutaneous, branchopulmonary, intestinal and joint conditions. Another method of treatment involves symptomatic care, bed rest, iodine therapy, aerosol nystatin and amphotericin B. Azole drugs including isoconazole and clotrimazole are used for geotrichosis treatment. Associated treatment for pulmonary geotrichosis includes the use of potassium iodide, sulfonamides or colistin. The associated asthma can be treated with desensitization and prednisolone. Amphotericin B, clotrimazole and S-fluorocytosine have become more susceptible to "G. candidum". Antimycotic resistance can appear due to repeated treatment.

Treatment can include topical steroids to diminish the inflammation. Antibiotics to diminish the proportion of aerobic bacteria is still a matter of debate. The use of local antibiotics, preferably local non-absorbed and broad spectrum, covering enteric gram-positive and gram-negative aerobes, can be an option. In some cases, systemic antibiotics can be helpful, such as amoxicillin/clavulanate or moxifloxacin. Vaginal rinsing with povidone iodine can provide relief of symptoms but does not provide long-term reduction of bacterial loads. Dequalinium chloride can also be an option for treatment.

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.

The cause of the infection determines the appropriate treatment. It may include oral or topical antibiotics and/or antifungal creams, antibacterial creams, or similar medications. A cream containing cortisone may also be used to relieve some of the irritation. If an allergic reaction is involved, an antihistamine may also be prescribed. For women who have irritation and inflammation caused by low levels of estrogen (postmenopausal), a topical estrogen cream might be prescribed.

The following are typical treatments for trichomoniasis, bacterial vaginosis, and yeast infections:

- Trichomoniasis: Single oral doses of either metronidazole, or tinidazole. "Sexual partner(s) should be treated simultaneously. Patients should be advised to avoid sexual intercourse for at least 1 week and until they and their partner(s) have completed treatment and follow-up."

- Bacterial vaginosis: The most commonly used antibiotics are metronidazole, available in both pill and gel form, and clindamycin available in both pill and cream form.

- Yeast infections: Local azole, in the form of ovula and cream. All agents appear to be equally effective. These anti-fungal medications, which are available in over the counter form, are generally used to treat yeast infections. Treatment may last anywhere between one, three, or seven days.

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.

Itraconazole given orally is the treatment of choice for most forms of the disease. Ketoconazole may also be used. Cure rates are high, and the treatment over a period of months is usually well tolerated. Amphotericin B is considerably more toxic, and is usually reserved for immunocompromised patients who are critically ill and those with central nervous system disease. Patients who cannot tolerate deoxycholate formulation of Amphotericin B can be given lipid formulations. Fluconazole has excellent CNS penetration and is useful where there is CNS involvement after initial treatment with Amphotericin B.

Uncomplicated infections can be diagnosed and treated based on symptoms alone. Antibiotics taken by mouth such as trimethoprim/sulfamethoxazole (TMP/SMX), nitrofurantoin, or fosfomycin are typically first line. Cephalosporins, amoxicillin/clavulanic acid, or a fluoroquinolone may also be used. However, resistance to fluoroquinolones among the bacterial that cause urinary infections has been increasing. The FDA recommends against the use of fluoroquinolones when other options are available due to higher risks of serious side effects. These medications substantially shorten the time to recovery with all being equally effective. A three-day treatment with trimethoprim, TMP/SMX, or a fluoroquinolone is usually sufficient, whereas nitrofurantoin requires 5–7 days. Fosfomycin may be used as a single dose but has been associated with lower rates of efficacy.

With treatment, symptoms should improve within 36 hours. About 50% of people will recover without treatment within a few days or weeks. Fluoroquinolones are not recommended as a first treatment. The Infectious Diseases Society of America states this due to the concern of generating resistance to this class of medication. Amoxicillin-clavulanate appears less effective than other options. Despite this precaution, some resistance has developed to all of these medications related to their widespread use. Trimethoprim alone is deemed to be equivalent to TMP/SMX in some countries. For simple UTIs, children often respond to a three-day course of antibiotics. Women with recurrent simple UTIs may benefit from self-treatment upon occurrence of symptoms with medical follow-up only if the initial treatment fails.

Treatment is typically with the antibiotics metronidazole or clindamycin. They can be either given by mouth or applied inside the vagina. About 10% to 15% of people, however, do not improve with the first course of antibiotics and recurrence rates of up to 80% have been documented. Recurrence rates are increased with sexual activity with the same pre-/posttreatment partner and inconsistent condom use although estrogen-containing contraceptives decrease recurrence. When clindamycin is given to pregnant women symptomatic with BV before 22 weeks of gestation the risk of pre-term birth before 37 weeks of gestation is lower.

Other antibiotics that may work include macrolides, lincosamides, nitroimidazoles, and penicillins.

Bacterial vaginosis is not considered a sexually transmitted infection, and treatment of a male sexual partner of a woman with bacterial vaginosis is not recommended.

The mainstay of treatment is antibiotics. Phenazopyridine is occasionally prescribed during the first few days in addition to antibiotics to help with the burning and urgency sometimes felt during a bladder infection. However, it is not routinely recommended due to safety concerns with its use, specifically an elevated risk of methemoglobinemia (higher than normal level of methemoglobin in the blood). Acetaminophen (paracetamol) may be used for fevers. There is no good evidence for the use of cranberry products for treating current infections.

In the majority of immunocompetent individuals, histoplasmosis resolves without any treatment. Antifungal medications are used to treat severe cases of acute histoplasmosis and all cases of chronic and disseminated disease. Typical treatment of severe disease first involves treatment with amphotericin B, followed by oral itraconazole.

Liposomal preparations of amphotericin B are more effective than deoxycholate preparations. The liposomal preparation is preferred in patients that might be at risk of nephrotoxicity, although all preparations of amphotericin B have risk of nephrotoxicity. Individuals taking amphotericin B are monitored for renal function.

Treatment with itraconazole will need to continue for at least a year in severe cases, while in acute pulmonary histoplasmosis, 6 to 12 weeks treatment is sufficient. Alternatives to itraconazole are posaconazole, voriconazole, and fluconazole. Individuals taking itraconazole are monitored for hepatic function.

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%.

A 2009 Cochrane review found tentative but insufficient evidence for probiotics as a treatment for BV. A 2014 review reached the same conclusion. A 2013 review found some evidence supporting the use of probiotics during pregnancy. The preferred probiotics for BV are those containing high doses of lactobacilli (around 10 ) given in the vagina. Intravaginal administration is preferred to taking them by mouth. Prolonged repetitive courses of treatment appear to be more promising than short courses.

Antivirals such as acyclovir, famciclovir, or valacyclovir may be used. Intravenous acyclovir is reserved for individuals who cannot swallow due to the pain, individuals with other systemic manifestations of herpes or severely immunocompromised individuals.