Stage I of the condition is usually treated with pentamidine or suramin through intramuscular injection or intravenous infusion if sufficient observation is possible. Stage II of the disease is typically treated with melarsoprol or eflornithine preferably introduced to the body intravenously. Both pentamidine and suramin have limited side effects. Melarsoprol is extremely effective but has many serious side effects which can cause neurological damage to a patient, however, the drug is often a patient's last hope in many late stage cases. Eflornithine is extremely expensive but has side effects that may be treated with ease. In regions of the world where the disease is common eflornithine is provided for free by the World Health Organization.

For "T. b. gambiense" the combination of nifurtimox and eflornithine (NECT) or eflornithine alone appear to be more effective and result in fewer side effects. These treatments may replace melarsoprol when available with the combination being first line. NECT has the benefit of requiring less injections of eflornithine.

Intravenous melarsoprol was previously the standard treatment for second-stage (neurological phase) disease and is effective for both types. Melarsoprol is the only treatment for second stage "T. b. rhodesiense"; however, it causes death in 5% of people who take it. Resistance to melarsoprol can occur.

The current treatment for first-stage disease is intravenous or intramuscular pentamidine for "T. b. gambiense" or intravenous suramin for "T. b. rhodesiense".

The use of trypanotolerant breeds for livestock farming should be considered if the disease is widespread.

Fly control is another option but is difficult to implement.

The main approaches to controlling African trypanosomiasis are to reduce the reservoirs of infection and the presence of the tsetse fly. Screening of people at risk helps identify patients at an early stage. Diagnosis should be made as early as possible and before the advanced stage to avoid complicated, difficult and risky treatment procedures.

If the outbreak is detected early, the organism can be destroyed by quarantines, movement controls, and maybe even put infected animals under euthanasia medication. Tsetse fly populations can be reduced or eliminated by traps, insecticides, and by treating infected animals with antiparasitic drugs. The Tse Tse habitat can be destroyed by alteration of vegetation so they can no longer live there.There are some drugs available that can prevent trypanosomiasis called prophylactic drugs.These drugs are very effective to protect animals during the times they are exposed to challenged diseases. Since they have been around for so long, some were not properly used which caused resistance to these drugs in some places.

As with many diseases in developing nations, (including trypanosomiasis and malaria) effective and affordable chemotherapy is sorely lacking and parasites or insect vectors are becoming increasingly resistant to existing anti-parasite drugs. Possibly due to the lack of financial return, new drugs are slow to emerge and much of the basic research into potential drug targets takes place in universities, funded by charitable organizations. Product Development Partnerships (PDPs) like Drugs for Neglected Diseases "initiatives" also work on the development of new treatments (combination treatments and new chemical entities) for visceral leishmaniasis.

The traditional treatment is with pentavalent antimonials such as sodium stibogluconate and meglumine antimoniate. Resistance is now common in India, and rates of resistance have been shown to be as high as 60% in parts of Bihar, India.

The treatment of choice for visceral leishmaniasis acquired in India is now Amphotericin B in its various liposomal preparations. In East Africa, the WHO recommended treatment is SSG&PM (sodium stibogluconate and paromomycin) developed by Drugs for Neglected Diseases "initiative" (DNDi)in 2010.

Miltefosine is the first oral treatment for this disease. The cure rate of miltefosine in Phase III clinical trials is 95%; Studies in Ethiopia show that is also effective in Africa. In HIV immunosuppressed people which are coinfected with leishmaniasis it has shown that even in resistant cases 2/3 of the people responded to this new treatment.

Miltefosine has received approval by the Indian regulatory authorities in 2002, in Germany in 2004 and in U.S.A. in 2014. It is now registered in many countries.

The drug is generally better tolerated than other drugs. Main side effects are gastrointestinal disturbance in the first or second day of treatment (a course of treatment is 28 days) which does not affect the efficacy. Because it is available as an oral formulation, the expense and inconvenience of hospitalization is avoided, and outpatient distribution of the drug becomes an option, making Miltefosine a drug of choice.

Incomplete treatment has been cited as a major reason of death from visceral leishmaniasis.

The nonprofit Institute for OneWorld Health has adopted the broad spectrum antibiotic paromomycin for use in treating VL; its antileishmanial properties were first identified in the 1980s. A treatment with paromomycin costs about $15 USD. The drug had originally been identified in the 1960s. The Indian government approved paromomycin for sale and use in August 2006.

There is currently no treatment for AHS.

Control of an outbreak in an endemic region involves quarantine, vector control and vaccination. To prevent this disease, the affected horses are usually slaughtered, and the uninfected horses are vaccinated against the virus. Three vaccines currently exist, which include a polyvalent vaccine, a monovalent vaccine, and a monovalent inactivated vaccine. This disease can also be prevented by destroying the insect vector habitats using insecticides.

There are no vaccines or preventive drugs for visceral leishmaniasis. The most effective method to prevent infection is to protect from sand fly bites. To decrease the risk of being bitten, these precautionary measures are suggested:

- Outdoors:

1. Avoid outdoor activities, especially from dusk to dawn, when sand flies generally are the most active.

2. When outdoors (or in unprotected quarters), minimize the amount of exposed (uncovered) skin to the extent that is tolerable in the climate. Wear long-sleeved shirts, long pants, and socks; and tuck your shirt into your pants.

3. Apply insect repellent to exposed skin and under the ends of sleeves and pant legs. Follow the instructions on the label of the repellent. The most effective repellents generally are those that contain the chemical DEET (N,N-diethylmetatoluamide).

- Indoors:

1. Stay in well-screened or air-conditioned areas.

2. Keep in mind that sand flies are much smaller than mosquitoes and therefore can get through smaller holes.

3. Spray living/sleeping areas with an insecticide to kill insects.

4. If you are not sleeping in a well-screened or air-conditioned area, use a bed net and tuck it under your mattress. If possible, use a bed net that has been soaked in or sprayed with a pyrethroid-containing insecticide. The same treatment can be applied to screens, curtains, sheets, and clothing (clothing should be retreated after five washings)."

On February 2012, the nonprofit Infectious Disease Research Institute launched a clinical trial of the visceral leishmaniasis vaccine. The vaccine is a recombinant form of two fused Leishmania parasite proteins with an adjuvant. Two phase 1 clinical trials with healthy volunteers are to be conducted. The first one takes place in Washington (state) and is followed by a trial in India.

Some of the strategies for controlling tropical diseases include:

- Draining wetlands to reduce populations of insects and other vectors, or introducing natural predators of the vectors.

- The application of insecticides and/or insect repellents) to strategic surfaces such as clothing, skin, buildings, insect habitats, and bed nets.

- The use of a mosquito net over a bed (also known as a "bed net") to reduce nighttime transmission, since certain species of tropical mosquitoes feed mainly at night.

- Use of water wells, and/or water filtration, water filters, or water treatment with water tablets to produce drinking water free of parasites.

- Sanitation to prevent transmission through human waste.

- In situations where vectors (such as mosquitoes) have become more numerous as a result of human activity, a careful investigation can provide clues: for example, open dumps can contain stagnant water that encourage disease vectors to breed. Eliminating these dumps can address the problem. An education campaign can yield significant benefits at low cost.

- Development and use of vaccines to promote disease immunity.

- Pharmacologic pre-exposure prophylaxis (to prevent disease before exposure to the environment and/or vector).

- Pharmacologic post-exposure prophylaxis (to prevent disease after exposure to the environment and/or vector).

- Pharmacologic treatment (to treat disease after infection or infestation).

- Assisting with economic development in endemic regions. For example, by providing microloans to enable investments in more efficient and productive agriculture. This in turn can help subsistence farming to become more profitable, and these profits can be used by local populations for disease prevention and treatment, with the added benefit of reducing the poverty rate.

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They are treated with antiprotozoal agents. Recent papers have also proposed the use of viruses to treat infections caused by protozoa.

The best treatment for cutaneous leishmaniasis is not known. Treatments that work for one species of leishmania may not work for another; it is recommended that advice of a tropical medicine or geographical medicine specialist be sought. Ideally, every effort should be made to establish the species of leishmania by molecular techniques (PCR) prior to starting treatment. In the setting of a developing country, there is often only one species present in a particular locality, so it is usually unnecessary to speciate every infection. Unfortunately, leishmaniasis is an orphan disease in developed nations, and almost all the current treatment options are toxic with significant side effects. The most sound treatment for cutaneous leishmaniasis thus far is prevention.

- "Leishmania major" :"L. major" infections are usually considered to heal spontaneously and do not require treatment, but there have been several reports of severe cases caused by "L. major" in Afghanistan. In Saudi Arabia, a six-week course of oral fluconazole 200 mg daily has been reported to speed up healing. In a randomized clinical trial from Iran, fluconazole 400 mg daily was shown to be significantly more effective than fluconazole 200 mg daily in the treatment of cutaneous leishmaniasis.

- "Leishmania braziliensis" :Treatment with pentavalent antimonials or amphotericin is necessary, because of the risk of developing disfiguring mucocutaneous lesions.

- "Leishmania infantum" :"L. infantum" causes cutaneous leishmaniasis in southern France.

New treatment options are arising from the new oral drug miltefosine (Impavido) which has shown in several clinical trials to be very efficient and safe in visceral and cutaneous leishmaniasis. Recent studies from Bolivia show a high cure rate for mucocutaneous leishmaniasis. Comparative studies against pentavalent antimonials in Iran and Pakistan are also beginning to show a high cure rate for "L. major" and "L. tropica". It is registered in many countries of Latin America, as well in Germany. In October 2006 it received orphan drug status from the US Food and Drug administration. The drug is generally better tolerated than other drugs. Main side effects are gastrointestinal disturbances in the 1–2 days of treatment which does not affect the efficacy.

Secondary bacterial infection (especially with "Staphylococcus aureus") is common and may require antibiotics. Clinicians who are unfamiliar with cutaneous leishmaniasis may mistake the lesion for a pure bacterial infection (especially after isolation of "S. aureus" from bacterial skin swabs) and fail to consider the possibility of leishmaniasis.

Treatment is normally by a single intramuscular injection of penicillin, or by a course of penicillin, erythromycin or tetracycline tablets. A single oral dose of azithromycin was shown to be as effective as intramuscular penicillin. Primary and secondary stage lesions may heal completely, but the destructive changes of tertiary yaws are largely irreversible.

Biotechnology companies in the developing world have targeted neglected tropical diseases due to need to improve global health.

Mass drug administration is considered a possible method for eradication, especially for lymphatic filariasis, onchocerciasis, and trachoma, although drug resistance is a potential problem. According to Fenwick, Pfizer donated 70 million doses of drugs in 2011 to eliminate trachoma through the International Trachoma Initiative. Merck has helped The African Programme for the Control of Onchocerciasis (APOC) and Oncho Elimination Programme for the Americas to greatly diminished the effect of Onchocerciasis by donating ivermectin. Merck KGaA pledged to give 200 million tablets of praziquantel over 10 years, the only cure for schistosomiasis. GlaxoSmithKline has donated two billion tablets of medicine for lymphatic filariasis and pledged 400 million deworming tablets per year for five years in 2010. Johnson & Johnson has pledged 200 million deworming tablets per year. Novartis has pledged leprosy treatment, EISAI pledged two billion tablets to help treat lymphatic filariasis.

Lymphatic filariasis is also known as elephantiasis. There are approximately 120 million individuals infected and 40 million with deformities. Approximately two-thirds of cases are in Southwest Asia and one-third in Africa. Lymphatic filariasis is rarely fatal. Lymphatic filariasis has lifelong implications, such as lymphoedema of the limbs, genital disease, and painful recurrent attacks. Most people are asymptomatic, but have lymphatic damage. Up to 40 percent of infected individuals have kidney damage. It is a vector-borne disease, caused by nematode worms that are transmitted by mosquitoes.

It can be treated with cost-effective antihelminthic treatments, and washing skin can slow or even reverse damage. It is diagnosed with a finger-prick blood test.

Animal trypanosomiasis, also known as nagana and nagana pest, or sleeping sickness, is a disease of vertebrates. The disease is caused by trypanosomes of several species in the genus "Trypanosoma" such as "Trypanosoma brucei". "Trypanosoma vivax" causes nagana mainly in West Africa, although it has spread to South America. The trypanosomes infect the blood of the vertebrate host, causing fever, weakness, and lethargy, which lead to weight loss and anemia; in some animals the disease is fatal unless treated. The trypanosomes are transmitted by tsetse flies.

An interesting feature is the remarkable tolerance to nagana pathology shown by some breeds of cattle, notably the N'Dama – a West African "Bos taurus" breed. This contrasts with the susceptibility shown by East African "Bos indicus" cattle such as the zebu.

One study using the medicinal plant "Peganum harmala" showed it to have a lifesaving effect on cattle infected with East Coast fever.

The classical treatment with tetracyclines (1970–1990) cannot provide efficiency more than 50%.

Since the early 1990s, buparvaquone is used in bovine theileriosis with remarkable results (90 to 98% recovery).

Other than the buparvaquones, other chemotherapeutic options are the parvaquones, e.g. Clexon. Halofuginone lactate has also been shown to have an 80.5% efficacy against "Theirelia parva parva" infections. The ultimate factor that causes death is pulmonary edema.

In May 2010, a vaccine to protect cattle against East Coast fever reportedly had been approved and registered by the governments of Kenya, Malawi and Tanzania. This consists of cryopreserved sporozoites from crushed ticks, but it is expensive and can cause disease.

Control of the disease relies on control of ticks of domestic animals, particularly disease-resistant ticks. This is a major concern in tropical countries with large livestock populations, especially in the endemic area. Pesticides (acaricides) are applied in dipping baths or spray races, and cattle breeds with good ability to acquire immune resistance to the vector ticks are used.

African horse sickness was diagnosed in Spain in 1987–90 and in Portugal in 1989, but was eradicated using slaughter policies, movement restrictions, vector eradication, and vaccination.

African tick bite fever is usually mild, and most patients do not need more than at-home treatment with antibiotics for their illness. However, because so few patients with this infection visit a doctor, the best antibiotic choice, dose and length of treatment are not well known. Typically doctors treat this disease with antibiotics that have been used effectively for the treatment of other diseases caused by bacteria of similar species, such as Rocky Mountain Spotted Fever.

For mild cases, people are usually treated with one of the following:

- doxycycline

- chloramphenicol

- ciprofloxacin

If a person has more severe symptoms, like a high fever or serious headache, the infection can be treated with doxycycline for a longer amount of time. Pregnant women should not use doxycycline or ciprofloxacin as both antibiotics can cause problems in fetuses. Josamycin has been used effectively for treatment of pregnant women with other rickettsial diseases, but it is unclear if it has a role in the treatment of ATBF.

Currently, no specific treatment for chikungunya is available. Supportive care is recommended, and symptomatic treatment of fever and joint swelling includes the use of nonsteroidal anti-inflammatory drugs such as naproxen, non-aspirin analgesics such as paracetamol (acetaminophen) and fluids. Aspirin is not recommended due to the increased risk of bleeding. Despite anti-inflammatory effects, corticosteroids are not recommended during the acute phase of disease, as they may cause immunosuppression and worsen infection.

Passive immunotherapy has potential benefit in treatment of chikungunya. Studies in animals using passive immunotherapy have been effective, and clinical studies using passive immunotherapy in those particularly vulnerable to severe infection are currently in progress. Passive immunotherapy involves administration of anti-CHIKV hyperimmune human intravenous antibodies (immunoglobulins) to those exposed to a high risk of chikungunya infection. No antiviral treatment for chikungunya virus is currently available, though testing has shown several medications to be effective "in vitro".

The use of antifungals and heat-induced therapy has been suggested as a treatment of "B. dendrobatidis." " "However, some of these antifungals may cause adverse skin effects on certain species of frogs. And although we do use them to treat species that are infected by chytridiomycosis, the infection never fully eradicates. A study done by Rollins-Smith and colleagues suggests that itraconazole is the antifungal of choice when it comes to treatment of "Bd." This is favored in comparison to amphotericin B and chloramphenicol because of their toxicity, specifically chloramphenicol as it is correlated with leukemia in toads. This becomes a difficult situation because without treatment, frogs will suffer from limb deformities and even death, but may also suffer skin abnormalities with treatment. Treatment of chytridiomycosis isn’t always successful, and some frogs are not able to handle the treatment process. It is important to consult with a veterinarian before treating frogs that suffer from chytridiomycosis"."

Individuals infected with "B. dendrobatidis" are bathed in intraconazole solutions, and within a few weeks, previously infected individuals test negative for "B. dendrobatidis" using PCR assays. Heat therapy is also used to neutralize "B. dendrobatidis" in infected individuals. Temperature-controlled laboratory experiments are used to increase the temperature of an individual past the optimal temperature range of "B. dendrobatidis". Experiments, where the temperature is increased beyond the upper bound of the "B. dendrobatidis" optimal range of 25 to 30 °C, show its presence will dissipate within a few weeks and individuals infected return to normal. Formalin/malachite green has also been used to successfully treat individuals infected with chytridiomycosis. An Archey's frog was successfully cured of chytridiomycosis by applying chloramphenicol topically. However, the potential risks of using antifungal drugs on individuals are high.

The term Winterbottom's sign derives from descriptions of the posterior cervical lymphadenopathy associated with African trypanosomiasis made by a slave trader using the sign to weed out the ill.

The treatment of melioidosis is divided into two stages, an intravenous high-intensity phase and an eradication phase to prevent recurrence.

- Intravenous intensive phase

- Eradication phase

It is currently thought that it may be possible to eradicate yaws although it is not certain that humans are the only reservoir of infection. A single injection of long-acting penicillin or other beta lactam antibiotic cures the disease and is widely available; and the disease is believed to be highly localised.

In April 2012, WHO initiated a new global campaign for the eradication of yaws, which has been on the WHO eradication list since 2011. According to the official roadmap, elimination should be achieved by 2020.

Prior to the most recent WHO campaign, India launched its own national yaws elimination campaign which appears to have been successful.

Certification for disease-free status requires an absence of the disease for at least five years. In India this happened on 19 September 2011. In 1996 there were 3,571 yaws cases in India; in 1997 after a serious elimination effort began the number of cases fell to 735. By 2003 the number of cases was 46. The last clinical case in India was reported in 2003 and the last latent case in 2006. India is a country where yaws is now considered to have been eliminated

In March 2013, WHO convened a new meeting of yaws experts in Geneva to further discuss the strategy of the new eradication campaign. The meeting was significant, and representatives of most countries where yaws is endemic attended and described the epidemiological situation at the national level. The disease is currently known to be present in Indonesia and Timor-Leste in South-East Asia; Papua New Guinea, the Solomon Islands and Vanuatu in the Pacific region; and Benin, Cameroon, Central African Republic, Congo, Côte d'Ivoire, Democratic Republic of Congo, Ghana and Togo in Africa. As reported at the meeting, in several such countries, mapping of the disease is still patchy and will need to be completed before any serious eradication effort could be enforced.

In those who have more than two weeks of arthritis, ribavirin may be useful. The effect of chloroquine is not clear. It does not appear to help acute disease, but tentative evidence indicates it might help those with chronic arthritis. Steroids do not appear to be an effective treatment. NSAIDs and simple analgesics can be used to provide partial symptom relief in most cases. Methotrexate, a drug used in the treatment of rheumatoid arthritis, has been shown to have benefit in treating inflammatory polyarthritis resulting from chikungunya, though the drug mechanism for improving viral arthritis is unclear.

Surgical drainage is usually indicated for prostatic abscesses and septic arthritis, may be indicated for parotid abscesses, and is not usually indicated for hepatosplenic abscesses. In bacteraemic melioidosis unresponsive to intravenous antibiotic therapy, splenectomy has been attempted, but only anecdotal evidence supports this practice.