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.

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.

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.

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.

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.

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.

Herpetic stromal keratitis is treated initially with prednisolone drops every 2 hours

accompanied by a prophylactic antiviral drug: either topical antiviral or an oral agent such as acyclovir or valacyclovir. The prednisolone drops are tapered every 1–2 weeks depending on the degree of clinical improvement. Topical antiviral medications are not absorbed by the cornea through an intact epithelium, but orally administered acyclovir penetrates an intact cornea and anterior chamber. In this context, oral acyclovir might benefit the deep corneal inflammation of disciform keratitis.

Treatment includes artificial tears and eye lubricants, stopping toxic medications, performing punctal occlusion, bandage contact lens and amniotic membrane transplant. These measures intend to improve corneal epithelial healing.

Mast cell stabilizers can help people with allergic conjunctivitis. They tend to have delayed results, but they have fewer side-effects than the other treatments and last much longer than those of antihistamines. Some people are given an antihistamine at the same time so that there is some relief of symptoms before the mast cell stabilizers becomes effective. Doctors commonly prescribe lodoxamide and nedocromil as mast cell stabilizers, which come as eye drops.

A mast cell stabilizer is a class of non-steroid controller medicine that reduces the release of inflammation-causing chemicals from mast cells. They block a calcium channel essential for mast cell degranulation, stabilizing the cell, thus preventing the release of histamine. Decongestants may also be prescribed. Another common mast cell stabilizer that is used for treating allergic conjunctivitis is sodium cromoglicate.

Antihistamines such as diphenhydramine and chlorpheniramine are commonly used as treatment. People treated with H1 antihistamines exhibit reduced production of histamine and leukotrienes as well as downregulation of adhesion molecule expression on the vasculature which in turn attenuates allergic symptoms by 40–50%.

Dual-action medications are also prescribed frequently. Olopatadine (Patanol) and ketotifen fumarate (Alaway or Zaditor) both provide protection by acting as an antihistamine and a mast cell stabilizer together. Patanol is a prescription medication, whereas ketotifen fumarate is not.

A systematic review of 30 trials, with 17 different treatment comparisons found that all topical antihistamines and mast cell stabilizers included for comparison were effective in reducing symptoms of seasonal allergic conjunctivitis. There was not enough evidence to determine differences in long-term efficacy among the treatments.

Many of the eye drops can cause burning and stinging, and have side-effects. Proper eye hygiene can improve symptoms, especially with contact lenses. Avoiding precipitants, such as pollen or mold can be preventative.

Antibiotics are commonly used to prevent secondary bacterial infection. There are no specific antiviral drugs in common use at this time for FVR, although one study has shown that ganciclovir, PMEDAP, and cidofovir hold promise for treatment. More recent research has indicated that systemic famciclovir is effective at treating this infection in cats without the side effects reported with other anti-viral agents. More severe cases may require supportive care such as intravenous fluid therapy, oxygen therapy, or even a feeding tube. Conjunctivitis and corneal ulcers are treated with topical antibiotics for secondary bacterial infection.

Lysine is commonly used as a treatment, however in a 2015 systematic review, where the authors investigated all clinical trials with cats as well as "in vitro" studies, concluded that lysine supplementation is not effective for the treatment or prevention of feline herpesvirus 1 infection.

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%.

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.

Shade, insect repellent-impregnated ear tags, and lower stocking rates may help prevent IBK. Early identification of the disease also helps prevent spread throughout the herd. Treatment is with early systemic use of a long-acting antibiotic such as tetracycline or florfenicol. Subconjunctival injections with procaine penicillin or other antibiotics are also effective, providing a "bubble" of antibiotic which releases into the eye slowly over several days.

Anti-inflammatory therapy can help shorten recovery times, but topical corticosteroids should be used with care if corneal ulcers are present.

"M. bovis" uses several different serotyped fimbriae as virulence factors, consequently pharmaceutical companies have exploited this to create vaccines. However, currently available vaccines are not reliable.

For mild cases, over-the-counter wart medicines, such as salicylic acid may shorten infection duration. Daily topical application of tretinoin cream may also trigger resolution. These treatments require several months for the infection to clear, and are often associated with intense inflammation and possibly discomfort.

Studies have found cantharidin to be an effective and safe treatment for removing molluscum contagiosum. This medication is usually well-tolerated though mild side effects such as pain or blistering are common.

There is no high-quality evidence for cimetidine. However, oral cimetidine has been used as alternative treatment for pediatric population as it is more difficult to use more invasive and discomforting application.

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.

Because molluscum contagiosum is usually self-limiting (resolving without treatment) and treatment options can cause discomfort to children, initial recommendations are often to simply wait for the lesions to resolve on their own. Current treatment options are invasive, requiring tissue destruction and patient discomfort.

Bumps located in the genital area may be treated in an effort to prevent them from spreading. When treatment has resulted in elimination of all bumps, the infection has been effectively cured and will not reappear unless the person is reinfected.

There is a vaccine for FHV-1 available (ATCvet code: , plus various combination vaccines), but although it limits or weakens the severity of the disease and may reduce viral shedding, it does not prevent infection with FVR. Studies have shown a duration of immunity of this vaccine to be at least three years. The use of serology to demonstrate circulating antibodies to FHV-1 has been shown to have a positive predictive value for indicating protection from this disease.

Ligneous conjunctivitis may be managed by topical treatments of plasminogen, topical and subconjunctival fresh frozen plasma, and fibrinolytic therapy.

Due to the different underlying causes, proper diagnosis, treatment, and prognosis can only be determined by an eye care professional. Punctate epithelial erosions may be treated with artificial tears. In some disorders, topical antibiotic is added to the treatment. Patients should discontinue contact lens wear until recovery.

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

Depending on severity, therapies may range from topical or oral anti-inflammatories to irrigation and surgical repair.

Treatment is possible with long-acting antibiotics, but milk from such cows is not marketable until drug residues have left the cow's system. Antibiotics may be systemic (injected into the body), or they may be forced upwards into the teat through the teat canal (intramammary infusion). Cows being treated may be marked with tape to alert dairy workers, and their milk is syphoned off and discarded. To determine whether the levels of antibiotic residuals are within regulatory requirements, special tests exist. Vaccinations for mastitis are available, but as they only reduce the severity of the condition, and cannot prevent reoccurring infections, they should be used in conjunction with a mastitis prevention program.

"Taylorella equigenitalis" is susceptible to most antibiotics, although the carrier state in mares is difficult to eliminate. Most mares with acute endometritis recover spontaneously. Recommended therapy is to infuse the uterus with an antibiotic such as penicillin, cleansing the clitoral area with 2% chlorhexidine solution and then applying chlorhexidine or nitrofurazone ointment to the clitoral fossa and sinuses. The entire treatment is repeated daily for five days.

It is relatively easy to eliminate the carrier state in stallions using local disinfectant. With the stallion's penis dropped and the glans extended from the foreskin, the shaft of the penis, including the folds of the prepuce and the urethral fossa, should be cleansed daily for five days with a 2% chlorhexidine solution. After drying, nitrofurazone cream is applied to these areas.

Docosanol, a saturated fatty alcohol, is a safe and effective topical application that has been approved by the United States Food and Drug Administration for herpes labialis in adults with properly functioning immune systems. It is comparable in effectiveness to prescription topical antiviral agents. Due to its mechanism of action, there is little risk of drug resistance. The duration of symptoms can be shortened a bit if an antiviral, anesthetic, zinc oxide or zinc sulfate cream is applied soon after it starts.

Effective antiviral medications include acyclovir and penciclovir, which can speed healing by as much as 10%. Famciclovir or valacyclovir, taken in pill form, can be effective using a single day, high-dose application and is more cost effective and convenient than the traditional treatment of lower doses for 5–7 days.