The majority of time treatment is symptomatic. Specific treatments are effective for bacterial, fungal, and herpes simplex infections.

Gargling salt water is often suggested but evidence looking at its usefulness is lacking. Alternative medicines are promoted and used for the treatment of sore throats. However, they are poorly supported by evidence.

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.

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.

Corticosteroids, such as dexamethasone and budesonide, have been shown to improve outcomes in children with all severities of croup. Significant relief is obtained as early as six hours after administration. While effective when given by injection, or by inhalation, giving the medication by mouth is preferred. A single dose is usually all that is required, and is generally considered to be quite safe. Dexamethasone at doses of 0.15, 0.3 and 0.6 mg/kg appear to be all equally effective.

Antibiotic ointment is typically applied to the newborn's eyes within 1 hour of birth as prevention against gonococcal ophthalmia. This maybe erythromycin, tetracycline, or silver nitrate.

While other treatments for croup have been studied, none have sufficient evidence to support their use. Inhalation of hot steam or humidified air is a traditional self-care treatment, but clinical studies have failed to show effectiveness and currently it is rarely used. The use of cough medicines, which usually contain dextromethorphan or guaifenesin, are also discouraged. There is tentative evidence that breathing heliox (a mixture of helium and oxygen) to decrease the work of breathing is useful in those with severe disease. Since croup is usually a viral disease, antibiotics are not used unless secondary bacterial infection is suspected. In cases of possible secondary bacterial infection, the antibiotics vancomycin and cefotaxime are recommended. In severe cases associated with influenza A or B, the antiviral neuraminidase inhibitors may be administered.

It is extremely difficult to successfully treat BPF, mainly because of the difficulty obtaining a proper diagnosis. Since the disease starts out with what seems to be a common case of conjunctivitis, "H. aegyptius" is not susceptible to the antibiotic eye drops that are being used to treat it. This treatment is ineffective because it treats only the local ocular infection, whereas if it progresses to BPF, systemic antibiotic treatment is required. Although BPF is susceptible to many commonly used antibiotics, including ampicillin, cefuroxime, cefotaxime, rifampin, and chloramphenicol, by the time it is diagnosed the disease has progressed too much to be effectively treated. However, with the fast rate of progression of BPF it is unlikely that it will be successfully treated. With antibiotic therapy, the mortality rate of BPF is around 70%.

Prophylaxis needs antenatal, natal, and post-natal care.

- Antenatal measures include thorough care of mother and treatment of genital infections when suspected.

- Natal measures are of utmost importance as mostly infection occurs during childbirth. Deliveries should be conducted under hygienic conditions taking all aseptic measures. The newborn baby's closed lids should be thoroughly cleansed and dried.

- If it is determined that the cause is due to a blocked tear duct, a gentle palpation between the eye and the nasal cavity may be used to clear the tear duct. If the tear duct is not cleared by the time the newborn is one year old, surgery may be required.

- Postnatal measures include:

- Chemical ophthalmia neonatorum is a self-limiting condition and does not require any treatment.

- Gonococcal ophthalmia neonatorum needs prompt treatment to prevent complications. Topical therapy should include

Systemic therapy: Newborns with gonococcal ophthalmia neonatorum should be treated for seven days with one of the following regimens ceftriaxone, cefotaxime, ciprofloxacin, crystalline benzyl penicillin

- Other bacterial ophthalmia neonatorum should be treated by broad spectrum antibiotics drops and ointment for two weeks.

- Neonatal inclusion conjunctivitis caused by Chlamydia trachomatis responds well to topical tetracycline 1% or erythromycin 0.5% eye ointment QID for three weeks. However systemic erythromycin should also be given since the presence of chlamydia agents in conjunctiva implies colonization of upper respiratory tract as well. Both parents should also be treated with systemic erythromycin.

- Herpes simplex conjunctivitis should be treated with intravenous acyclovir for a minimum of 14 days to prevent systemic infection.

The basic method for control of the conjunctivitis includes proper hygiene and care for the affected eye. If the conjunctivitis is found to be caused by "H. aegyptius" Biogroup III then prompt antibiotic treatment preferably with rifampin has been shown to prevent progression to BPF. If the infected person resides in Brazil, it is mandatory that the infection is reported to the health authority so that a proper investigation of the contacts can be completed. This investigation will help to determine the probable source of the infection.

"Haemophilus influenzae" produces beta-lactamases, and it is also able to modify its penicillin-binding proteins, so it has gained resistance to the penicillin family of antibiotics.

In severe cases, cefotaxime and ceftriaxone delivered directly into the bloodstream are the elected antibiotics, and, for the less severe cases, an association of ampicillin and sulbactam, cephalosporins of the second and third generation, or fluoroquinolones are preferred. (Fluoroquinolone-resistant "Haemophilus influenzae" have been observed.)

Macrolide antibiotics (e.g., clarithromycin) may be used in patients with a history of allergy to beta-lactam antibiotics. Macrolide resistance has also been observed.

The serious complications of HiB are brain damage, hearing loss, and even death.

There is no treatment currently available. The virus generally resolves itself within a five to seven day period. The use of steroids can actually cause a corneal microbial superinfection which then requires antimicrobial therapy to eliminate.

The disease may remain manageable, but in more severe cases, lymph nodes in the neck may swell, and breathing and swallowing are more difficult. People in this stage should seek immediate medical attention, as obstruction in the throat may require intubation or a tracheotomy. Abnormal cardiac rhythms can occur early in the course of the illness or weeks later, and can lead to heart failure. Diphtheria can also cause paralysis in the eye, neck, throat, or respiratory muscles. Patients with severe cases are put in a hospital intensive care unit and given a diphtheria antitoxin. Since antitoxin does not neutralize toxin that is already bound to tissues, delaying its administration is associated with an increase in mortality risk. Therefore, the decision to administer diphtheria antitoxin is based on clinical diagnosis, and should not await laboratory confirmation.

Antibiotics have not been demonstrated to affect healing of local infection in diphtheria patients treated with antitoxin. Antibiotics are used in patients or carriers to eradicate "C. diphtheriae" and prevent its transmission to others. The Centers for Disease Control and Prevention recommends either:

- Metronidazole

- Erythromycin is given (orally or by injection) for 14 days (40 mg/kg per day with a maximum of 2 g/d), or

- Procaine penicillin G is given intramuscularly for 14 days (300,000 U/d for patients weighing 10 kg); patients with allergies to penicillin G or erythromycin can use rifampin or clindamycin.

In cases that progress beyond a throat infection, diphtheria toxin spreads through the blood and can lead to potentially life-threatening complications that affect other organs, such as the heart and kidneys. Damage to the heart caused by the toxin affects the heart's ability to pump blood or the kidneys' ability to clear wastes. It can also cause nerve damage, eventually leading to paralysis. About 40% to 50% of those left untreated can die.

Empirical treatment should generally be started in a patient in whom suspicion of diphtheria is high.

Prescribing antibiotics for laryngitis is not suggested practice. The antibiotics penicillin V and erythromycin are not effective for treating acute laryngitis. Erythromycin may improve voice disturbances after one week and cough after two weeks, however any modest subjective benefit is not greater than the adverse effects, cost, and the risk of bacteria developing resistance to the antibiotics. Health authorities have been strongly encouraging physicians to decrease the prescribing of antibiotics to treat common upper respiratory tract infections because antibiotic usage does not significantly reduce recovery time for these viral illnesses. Decreased antibiotic usage could also have prevented drug resistant bacteria. Some have advocated a delayed antibiotic approach to treating URIs which seeks to reduce the consumption of antibiotics while attempting to maintain patient satisfaction. Most studies show no difference in improvement of symptoms between those treated with antibiotics right away and those with delayed prescriptions. Most studies also show no difference in patient satisfaction, patient complications, symptoms between delayed and no antibiotics. A strategy of "no antibiotics" results in even less antibiotic use than a strategy of "delayed antibiotics".

Severe cases will require admission to intensive care. In addition to the measures listed above for mild tetanus:

- Human tetanus immunoglobulin injected intrathecally (increases clinical improvement from 4% to 35%)

- Tracheotomy and mechanical ventilation for 3 to 4 weeks. Tracheotomy is recommended for securing the airway because the presence of an endotracheal tube is a stimulus for spasm

- Magnesium, as an intravenous (IV) infusion, to prevent muscle spasm

- Diazepam as a continuous IV infusion

- The autonomic effects of tetanus can be difficult to manage (alternating hyper- and hypotension hyperpyrexia/hypothermia) and may require IV labetalol, magnesium, clonidine, or nifedipine

Drugs such as diazepam or other muscle relaxants can be given to control the muscle spasms. In extreme cases it may be necessary to paralyze the patient with curare-like drugs and use a mechanical ventilator.

In order to survive a tetanus infection, the maintenance of an airway and proper nutrition are required. An intake of 3,500 to 4,000 calories and at least 150 g of protein per day is often given in liquid form through a tube directly into the stomach (percutaneous endoscopic gastrostomy), or through a drip into a vein (parenteral nutrition). This high-caloric diet maintenance is required because of the increased metabolic strain brought on by the increased muscle activity. Full recovery takes 4 to 6 weeks because the body must regenerate destroyed nerve axon terminals.

The Centers for Disease Control describe protocol for treating sinusitis while at the same time discouraging overuse of antibiotics:

- Target likely organisms with first-line drugs: Amoxicillin, Amoxicillin/Clavulanate

- Use shortest effective course: Should see improvement in 2–3 days. Continue treatment for 7 days after symptoms improve or resolve (usually a 10–14 day course).

- Consider imaging studies in recurrent or unclear cases: some sinus involvement is frequent early in the course of uncomplicated viral URI

Treatment comprises symptomatic support usually via analgesics for headache, sore throat and muscle aches. Moderate exercise in sedentary subjects with naturally acquired URTI probably does not alter the overall severity and duration of the illness. No randomized trials have been conducted to ascertain benefits of increasing fluid intake.

Mild cases of tetanus can be treated with:

- tetanus immunoglobulin (TIG), also called "tetanus antibodies" or "tetanus antitoxin." It can be given as intravenous therapy or by intramuscular injection.

- metronidazole IV for 10 days

- diazepam oral or IV

During an acute flare-up, therapy is targeted at reducing the inflammation present, and dilating the pupil. Mydriasis is important, as pupillary constriction is the primary reason for pain. Anti-inflammatory therapy is usually given both systemically, often in the form of flunixin meglumine, and topically, as prednisolone acetate. The mydriatic of choice is atropine. In the periods between acute attacks, no therapy has been shown to be beneficial.

The antibiotics erythromycin, clarithromycin, or azithromycin are typically the recommended treatment. Newer macrolides are frequently recommended due to lower rates of side effects. Trimethoprim-sulfamethoxazole (TMP/SMX) may be used in those with allergies to first-line agents or in infants who have a risk of pyloric stenosis from macrolides.

A reasonable guideline is to treat people age >1 year within 3 weeks of cough onset and infants age <1 year and pregnant women within 6 weeks of cough onset. If the person is diagnosed late, antibiotics will not alter the course of the illness, and even without antibiotics, they should no longer be spreading pertussis. Antibiotics when used early decrease the duration of infectiousness, and thus prevent spread. Short-term antibiotics (azithromycin for 3–5 days) are as effective as long-term treatment (erythromycin 10–14 days) in eliminating "B. pertussis" with fewer and less severe side effects.

People with pertussis are infectious from the beginning of the catarrhal stage (a runny nose, sneezing, low-grade fever, symptoms of the common cold) through the third week after the onset of paroxysms (multiple, rapid coughs) or until 5 days after the start of effective antimicrobial treatment.

Effective treatments of the cough associated with this condition have not been developed.

Antibiotics are aimed at gram positive bacteria. Medical attention should be sought if symptoms persist beyond 2–3 days.

Horses that suffer from this disease can never be considered cured, although they can be managed by careful use of the therapy described above, and fast detection of new flare-ups. If the disease is not properly treated, it will eventually lead to blindness.

While most cases require no treatment, therapy options include cryotherapy, application of a topical salicylic acid compound, surgical and laser ablation.

The management of rhinitis depends on the underlying cause.

For allergic rhinitis, intranasal corticosteroids are recommended. For severe symptoms intranasal antihistamines may be added.