Treatment of AIT involves antibiotic treatment. Based on the offending organism found on microscopic examination of the stained fine needle aspirate, the appropriate antibiotic treatment is determined. In the case of a severe infection, systemic antibiotics are necessary. Empirical broad spectrum antimicrobial treatment provides preliminary coverage for a variety of bacteria, including "S. aureus" and "S. pyogenes." Antimicrobial options include penicillinase-resistant penicillins (ex: cloxacillin, dicloxacillin) or a combination of a penicillin and a beta-lactamase inhibitor. However, in patients with a penicillin allergy, clindamycin or a macrolide can be prescribed. The majority of anaerobic organisms involved with AIT are susceptible to penicillin. Certain Gram-negative bacilli (ex: "Prevotella", "Fusobacteria", and "Porphyromonas") are exhibiting an increased resistance based on the production of beta-lactamase. Patients who have undergone recent penicillin therapy have demonstrated an increase in beta-lactamase-producing (anaerobic and aerobic) bacteria. Clindamycin, or a combination of metronidazole and a macrolide, or a penicillin combined with a beta-lactamase inhibitor is recommended in these cases. Fungal thyroiditis can be treated with amphotericin B and fluconazole. Early treatment of AIT prevents further complications. However, if antibiotic treatment does not manage the infection, surgical drainage is required. Symptoms or indications requiring drainage include continued fever, high white blood cell count, and continuing signs of localized inflammation. The draining procedure is also based on clinical examination or ultrasound/CT scan results that indicate an abscess or gas formation. Another treatment of AIT involves surgically removing the fistula. This treatment is often the option recommended for children. However, in cases of an antibiotic resistant infection or necrotic tissue, a lobectomy is recommended. If diagnosis and/or treatment is delayed, the disease could prove fatal.

The Infectious Disease Society of America (IDSA) recommends treating uncomplicated methicillin resistant staph aureus (MRSA) bacteremia with a 14-day course of intravenous vancomycin. Uncomplicated bacteremia is defined as having positive blood cultures for MRSA, but having no evidence of endocarditis, no implanted prostheses, negative blood cultures after 2–4 days of treatment, and signs of clinical improvement after 72 hrs.

The antibiotic treatment of choice for streptococcal and enteroccal infections differs by species. However, it is important to look at the antibiotic resistance pattern for each species from the blood culture to better treat infections caused by resistant organisms.

Treatment consists of antibiotic therapy aimed at the typical bacterial pathogens in addition to supportive care for any complications which might result from the infection itself such as hypotension or respiratory failure. A typical regimen will include intravenous antibiotics such as from the penicillin-group which is active against "Staphylococcus aureus" and an aminoglycoside for activity against Gram-negative bacteria. For particularly invasive infections, antibiotics to cover anaerobic bacteria may be added (such as metronidazole). Treatment is typically for two weeks and often necessitates insertion of a central venous catheter or peripherally inserted central catheter.

The treatment of gram negative bacteremia is also highly dependent on the causative organism. Empiric antibiotic therapy should be guided by the most likely source of infection and the patient's past exposure to healthcare facilities. In particular, a recent history of exposure to a healthcare setting may necessitate the need for antibiotics with "pseudomonas aeruginosa" coverage or broader coverage for resistant organisms. Extended generation cephalosporins such as ceftriaxone or beta lactam/beta lactam inhibitor antibiotics such as piperacillin-tazobactam are frequently used for the treatment of gram negative bacteremia.

A boil may clear up on its own without bursting, but more often it will need to be opened and drained. This will usually happen spontaneously within two weeks. Regular application of a warm moist compress, both before and after a boil opens, can help speed healing. The area must be kept clean, hands washed after touching it, and any dressings disposed of carefully, in order to avoid spreading the bacteria. A doctor may cut open or "lance" a boil to allow it to drain, but squeezing or cutting should not be attempted at home, as this may further spread the infection. Antibiotic therapy may be recommended for large or recurrent boils or those that occur in sensitive areas (such as the groin, breasts, armpits, around or in the nostrils, or in the ear). Antibiotics should not be used for longer than one month, with at least two months (preferably longer) between uses, otherwise it will lose its effectiveness. If the patient has chronic (more than two years) boils, removal by plastic surgery may be indicated.

Furuncles at risk of leading to serious complications should be incised and drained if antibiotics or steroid injections are not effective. These include furuncles that are unusually large, last longer than two weeks, or occur in the middle of the face or near the spine. Fever and chills are signs of sepsis and indicate immediate treatment is needed.

Staphylococcus aureus has the ability to acquire antimicrobial resistance easily, making treatment difficult. Knowledge of the antimicrobial resistance of "S. aureus" is important in the selection of antimicrobials for treatment.

Treatment depends on the type of opportunistic infection, but usually involves different antibiotics.

The infection is frequently penicillin resistant. There are a number of antibiotics options including amoxicillin/clavulanate, clindamycin, or metronidazole in combination with benzylpenicillin (penicillin G) or penicillin V. Piperacillin/tazobactam may also be used.

Treatment is by removing the pus, antibiotics, sufficient fluids, and pain medication. Steroids may also be useful. Admission to hospital is generally not needed.

During the 1950s there were outbreaks of omphalitis that then led to anti-bacterial treatment of the umbilical cord stump as the new standard of care. It was later determined that in developed countries keeping the cord dry is sufficient, (known as "dry cord care") as recommended by the American Academy of Pediatrics. The umbilical cord dries more quickly and separates more readily when exposed to air However, each hospital/birthing center has its own recommendations for care of the umbilical cord after delivery. Some recommend not using any medicinal washes on the cord. Other popular recommendations include triple dye, betadine, bacitracin, or silver sulfadiazine. With regards to the medicinal treatments, there is little data to support any one treatment (or lack thereof) over another. However one recent review of many studies supported the use of chlorhexidine treatment as a way to reduce risk of death by 23% and risk of omphalitis by anywhere between 27-56% in community settings in underdeveloped countries. This study also found that this treatment increased the time that it would take for the umbilical stump to separate or fall off by 1.7 days. Lastly this large review also supported the notion that in hospital settings no medicinal type of cord care treatment was better at reducing infections compared to dry cord care.

Individuals at higher risk are often prescribed prophylactic medication to prevent an infection from occurring. A patient's risk level for developing an opportunistic infection is approximated using the patient's CD4 T-cell count and sometimes other markers of susceptibility. Common prophylaxis treatments include the following:

If the tonsillitis is caused by group A streptococcus, then antibiotics are useful, with penicillin or amoxicillin being primary choices. Cephalosporins and macrolides are considered good alternatives to penicillin in the acute setting. A macrolide such as erythromycin is used for people allergic to penicillin. Individuals who fail penicillin therapy may respond to treatment effective against beta-lactamase producing bacteria such as clindamycin or amoxicillin-clavulanate. Aerobic and anaerobic beta lactamase producing bacteria that reside in the tonsillar tissues can "shield" group A streptococcus from penicillins.

Immediate treatment is very important for someone with orbital cellulitis. Treatment typically involves intravenous (IV) antibiotics in the hospital and frequent observation (every 4–6 hours). Along with this several laboratory tests are run including a complete blood count, differential, and blood culture.

- Antibiotic therapy – Since orbital cellulitis is commonly caused by "Staphylococcus" and "Streptococcus" species both penicillins and cephalosporins are typically the best choices for IV antibiotics. However, due to the increasing rise of MRSA (methicillin-resistant "Staphylococcus aureus") orbital cellulitis can also be treated with Vancomycin, Clindamycin, or Doxycycline. If improvement is noted after 48 hours of IV antibiotics, healthcare professions can then consider switching a patient to oral antibiotics (which must be used for 2–3 weeks).

- Surgical intervention – An abscess can threaten the vision or neurological status of a patient with orbital cellulitis, therefore sometimes surgical intervention is necessary. Surgery typically requires drainage of the sinuses and if a subperiosteal abscess is present in the medial orbit, drainage can be performed endoscopically. Post-operatively, patients must follow up regularly with their surgeon and remain under close observation.

This nitroimidazole compound, like metronidazole, has shown a marked therapeutic response in amoebic liver abscess. Occasional side effects include nausea and dizziness. Tinidazole is not widely available though it is more effective than metronidazole. Zuberi and Ibrahim found tinidazole to be effective in 86.7% cases of intestinal amoebiasis and in 100% cases of amoebic liver abscess.

Luminal amoebicides like halogenated oxyquinolines, e.g. diiodohydroxyquinoline in a dose of 0.6 G. thrice daily for 3 weeks, diloxanide furoate 0.5 G. three times a day for 10 days and sometimes tetracyclines 1–2 G./day for 5 days should be used concurrently with any of the above drugs as adjuncts to eliminate intestinal infection.

Chronic cases may be treated with tonsillectomy (surgical removal of tonsils) as a choice for treatment. Children have had only a modest benefit from tonsillectomy for chronic cases of tonsillitis.

For generations, the disease was treated with an application of the antiseptic gentian violet. Today, topical or oral antibiotics are usually prescribed. Mild cases may be treated with bactericidal ointment, such as mupirocin. In 95% of cases, a single antibiotic course results in resolution in children. It has been advocated that topical disinfectants are not nearly as efficient as antibiotics, and therefore should be avoided.

More severe cases require oral antibiotics, such as dicloxacillin, flucloxacillin, or erythromycin. Alternatively, amoxicillin combined with clavulanate potassium, cephalosporins (first-generation) and many others may also be used as an antibiotic treatment. Alternatives for people who are seriously allergic to penicillin or infections with MRSA include doxycycline, clindamycin, and SMX-TMP. When streptococci alone are the cause, penicillin is the drug of choice.

When the condition presents with ulcers, valacyclovir, an antiviral, may be given in case a viral infection is causing the ulcer.

Treatment is supportive and based upon symptoms, with fluid and electrolyte replacement as the primary goal. Dehydration caused by diarrhea and vomiting is the most common complication. To prevent dehydration, it is important to take frequent sips of a rehydration drink (like water) or try to drink a cup of water or rehydration drink for each large, loose stool.

Dietary management of enteritis consists of starting with a clear liquid diet until vomiting and diarrhea end and then slowly introduce the BRATT diet. The BRATT diet consists of bananas, rice, applesauce, tea, and toast. It is also important to avoid foods that are high in fiber or are possibly difficult to digest.

Although orbital cellulitis is considered an ophthalmic emergency the prognosis is good if prompt medical treatment is received.

In cases of viral adenoiditis, treatment with analgesics or antipyretics is often sufficient. Bacterial adenoiditis may be treated with antibiotics, such as amoxicillin - clavulanic acid or a cephalosporin. In case of adenoid hypertrophy, adenoidectomy may be performed to remove the adenoid.

Surgical debridement (cutting away affected tissue) is the mainstay of treatment for necrotizing fasciitis. Early medical treatment is often presumptive; thus, antibiotics should be started as soon as this condition is suspected. Given the dangerous nature of the disease, a high index of suspicion is needed. Initial treatment often includes a combination of intravenous antibiotics including piperacillin/tazobactam, vancomycin, and clindamycin. Cultures are taken to determine appropriate antibiotic coverage, and antibiotics may be changed when culture results are obtained.

Treatment for necrotizing fasciitis may involve an interdisciplinary care team. For example, in the case of a necrotizing fasciitis involving the head and neck, the team could include otolaryngologists, speech pathologists, intensivists, infectious disease specialists, and plastic surgeons or oral and maxillofacial surgeons. Maintaining strict asepsis during any surgical procedure and regional anaesthesia techniques is vital in preventing the occurrence of the disease.

Antibiotics are the first line of treatment in acute prostatitis. Antibiotics usually resolve acute prostatitis infections in a very short time, however a minimum of two to four weeks of therapy is recommended to eradicate the offending organism completely. Appropriate antibiotics should be used, based on the microbe causing the infection. Some antibiotics have very poor penetration of the prostatic capsule, others, such as ciprofloxacin, trimethoprim/sulfamethoxazole, and tetracyclines such as doxycycline penetrate prostatic tissue well. In acute prostatitis, penetration of the prostate is not as important as for category II because the intense inflammation disrupts the prostate-blood barrier. It is more important to choose a bactericidal antibiotic (kills bacteria, e.g., a fluoroquinolone antibiotic) rather than a bacteriostatic antibiotic (slows bacterial growth, e.g. tetracycline) for acute potentially life-threatening infections.

Severely ill patients may need hospitalization, while nontoxic patients can be treated at home with bed rest, analgesics, stool softeners, and hydration. Men with acute prostatitis complicated by urinary retention are best managed with a suprapubic catheter or intermittent catheterization. Lack of clinical response to antibiotics should raise the suspicion of an abscess and prompt an imaging study such as a transrectal ultrasound (TRUS).

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.

Systemic candidiasis occurs when Candida yeast enters the bloodstream and may spread (becoming disseminated candidiasis) to other organs, including the central nervous system, kidneys, liver, bones, muscles, joints, spleen, or eyes. Treatment typically consists of oral or intravenous antifungal medications. In candidal infections of the blood, intravenous fluconazole or an echinocandin such as caspofungin may be used. Amphotericin B is another option.

Hyperbaric oxygen treatment is sometimes used to treat necrotizing soft tissue infection in combination with antibiotics and debridement, but there is a lack of compelling evidence regarding its efficacy for this purpose.

There is not enough evidence to recommend alternative medicine such as tea tree oil or honey.

Most people who have an uncomplicated skin abscess should not use antibiotics. Antibiotics in addition to standard incision and drainage is recommended in persons with severe abscesses, many sites of infection, rapid disease progression, the presence of cellulitis, symptoms indicating bacterial illness throughout the body, or a health condition causing immunosuppression. People who are very young or very old may also need antibiotics. If the abscess does not heal only with incision and drainage, or if the abscess is in a place that is difficult to drain such as the face, hands, or genitals, then antibiotics may be indicated.

In those cases of abscess which do require antibiotic treatment, "Staphylococcus aureus" bacteria is a common cause and an anti-staphylococcus antibiotic such as flucloxacillin or dicloxacillin is used. The Infectious Diseases Society of America advises that the draining of an abscess is not enough to address community-acquired methicillin-resistant "Staphylococcus aureus" (MRSA), and in those cases, traditional antibiotics may be ineffective. Alternative antibiotics effective against community-acquired MRSA often include clindamycin, doxycycline, minocycline, and trimethoprim-sulfamethoxazole. The American College of Emergency Physicians advises that typical cases of abscess from MRSA get no benefit from having antibiotic treatment in addition to the standard treatment. If the condition is thought to be cellulitis rather than abscess, consideration should be given to possibility of strep species as cause that are still sensitive to traditional anti-staphylococcus agents such as dicloxacillin or cephalexin in patients able to tolerate penicillin. Antibiotic therapy alone without surgical drainage of the abscess is seldom effective due to antibiotics often being unable to get into the abscess and their ineffectiveness at low pH levels.

Culturing the wound is not needed if standard follow-up care can be provided after the incision and drainage. Performing a wound culture is unnecessary because it rarely gives information which can be used to guide treatment.