The usual recommendation for those needing iseikonic correction is to wear contact lenses. The effect of vertex distance is removed and the effect of center thickness is also almost removed, meaning there is minimal and likely unnoticeable image size difference. This is a good solution for those who can tolerate contact lenses.

Refractive surgery causes only minimal size differences, similar to contact lenses. In a study performed on 53 children who had amblyopia due to anisometropia, surgical correction of the anisometropia followed by strabismus surgery if required led to improved visual acuity and even to stereopsis in many of the children ("see:" Refractive surgery#Children).

Medication is used for strabismus in certain circumstances. In 1989, the US FDA approved Botulinum toxin therapy for strabismus in patients over 12 years old. Most commonly used in adults, the technique is also used for treating children, in particular children affected by infantile esotropia. The toxin is injected in the stronger muscle, causing temporary and partial paralysis. The treatment may need to be repeated three to four months later once the paralysis wears off. Common side effects are double vision, droopy eyelid, overcorrection, and no effect. The side effects typically resolve also within three to four months. Botulinum toxin therapy has been reported to be similarly successful as strabismus surgery for people with binocular vision and less successful than surgery for those who have no binocular vision.

Treatment is done by changing the optical magnification properties of the auxiliary optics (corrective lenses). The optical magnification properties of spectacle lenses can be adjusted by changing parameters like the base curve, vertex distance, and center thickness. Contact lenses may also provide a better optical magnification to reduce the difference in image size. The difference in magnification can also be eliminated by a combination of contact lenses and glasses (creating a weak telescope system). The optimum design solution will depend on different parameters like cost, cosmetic implications, and if the patient can tolerate wearing a contact lens.

Note however that before the optics can be designed, first the aniseikonia should be known=measured. When the image disparity is astigmatic (cylindrical) and not uniform, images can appear wider, taller, or diagonally different. When the disparity appears to vary across the visual field (field-dependent aniseikonia), as may be the case with an epiretinal membrane or retinal detachment, the aniseikonia cannot fully be corrected with traditional optical techniques like standard corrective lenses. However, partial correction often improves the patient's vision comfort significantly. Little is known yet about the possibilities of using surgical intervention to correct aniseikonia.

Treatment of strabismic or anisometropic amblyopia consists of correcting the optical deficit (wearing the necessary spectacle prescription) and often forcing use of the amblyopic eye, by patching the good eye, or instilling topical atropine in the good eye, or both.

Concerning patching versus atropine, a drawback is seen in using atropine; the drops can have a side effect of creating nodules in the eye which a correctional ointment can counteract. One should also be wary of overpatching or overpenalizing the good eye when treating amblyopia, as this can create so-called "reverse amblyopia". Eye patching is usually done on a part-time schedule of about 4–6 hours a day. Treatment is continued as long as vision improves. It is not worthwhile continuing to patch for more than 6 months if no improvement continues. Treatment of individuals age 9 through to adulthood is possible through applied perceptual learning.

Deprivation amblyopia is treated by removing the opacity as soon as possible followed by patching or penalizing the good eye to encourage the use of the amblyopic eye. The earlier the treatment is initiated, the easier and faster the treatment is and the less psychologically damaging. Also, the chance of achieving 20/20 vision is greater if treatment is initiated early.

One of the German public health insurance providers, Barmer, has changed its policy to cover, as of 1 April 2014, the costs for an app for amblyopic children whose condition has so far not improved through patching. The app offers dedicated eye exercises which the patient performs while wearing an eyepatch.

In cases of accommodative esotropia, the eyes turn inward due to the effort of focusing far-sighted eyes, and the treatment of this type of strabismus necessarily involves refractive correction, which is usually done via corrective glasses or contact lenses, and in these cases surgical alignment is considered only if such correction does not resolve the eye turn.

In case of strong anisometropia, contact lenses may be preferable to spectacles because they avoid the problem of visual disparities due to size differences (aniseikonia) which is otherwise caused by spectacles in which the refractive power is very different for the two eyes. In a few cases of strabismic children with anisometropic amblyopia, a balancing of the refractive error eyes via refractive surgery has been performed before strabismus surgery was undertaken.

Early treatment of strabismus when the person is a baby may reduce the chance of developing amblyopia and depth perception problems. However, a review of randomized controlled trials concluded that the use of corrective glasses to prevent strabismus is not supported by existing research. Most children eventually recover from amblyopia if they have had the benefit of patches and corrective glasses. Amblyopia has long been considered to remain permanent if not treated within a critical period, namely before the age of about seven years; however, recent discoveries give reason to challenge this view and to adapt the earlier notion of a critical period to account for stereopsis recovery in adults.

Eyes that remain misaligned can still develop visual problems. Although not a cure for strabismus, prism lenses can also be used to provide some temporary comfort and to prevent double vision from occurring.

Although the best outcome is achieved if treatment is started before age 8, children older than age 12 and some adults can show improvement in the affected eye. Children from 9 to 11 who wore an eye patch and performed near-point activities (vision therapy) were four times as likely to show a two-line improvement on a standard 11-line eye chart than children with amblyopia who did not receive treatment. Adolescents aged 13 to 17 showed improvement, as well, albeit to a lesser degree than younger children. Whether such improvements are only temporary, however, is uncertain, particularly if treatment is discontinued.

Tentative evidence shows that perceptual training may be beneficial in adults.

Virtual-reality computer games where each eye receives different signals of the virtual world that the player's brain must combine to successfully play the game have shown some promise in improving both monocularity in the affected eye, as well as binocularity.

In general, strabismus can be approached and treated with a variety of procedures. Depending on the individual case, treatment options include:

- Correction of refractive errors by glasses

- Prism therapy (if tolerated, to manage diplopia)

- Patching (mainly to manage amblyopia in children and diplopia in adults)

- Botulinum toxin injection

- Surgical correction

Surgical correction of the hypertropia is desired to achieve binocularity, manage diplopia and/or correct the cosmetic defect. Steps to achieve the same depend on mechanism of the hypertropia and identification of the offending muscles causing the misalignment. Various surgical procedures have been described and should be offered after careful examination of eyes, including a detailed orthoptic examination focussing on the disturbances in ocular motility and visual status. Specialty fellowship trained pediatric ophthalmologists and strabismus surgeons are best equipped to deal with these complex procedures.

Suppression may treated with vision therapy, though there is a wide range of opinions on long-term effectiveness between eye care professionals, with little scientific evidence of long-term improvement of suppression, if the underlying cause is not addressed (strabismus, amblyopia, etc.).

When this magnification difference becomes excessive the effect can cause diplopia, suppression, disorientation, eyestrain, headache, and dizziness and balance disorders.

Young children with strabismus normally suppress the visual field of one eye (or part of it), whereas adults who develop strabismus normally do not suppress and therefore suffer from double vision (diplopia). This also means that adults (and older children) have a higher risk of post-operative diplopia after undergoing strabismus surgery than young children. Patients who have undergone strabismus surgery at a young age often have monofixation syndrome (with peripheral binocular fusion and a central suppression scotoma).

Refractive errors such as hyperopia and Anisometropia may be associated abnormalities found in patients with vertical strabismus.

The vertical miscoordination between the two eyes may lead to

- Strabismic amblyopia, (due to deprivation / suppression of the deviating eye)

- cosmetic defect (most noticed by parents of a young child and in photographs)

- Face turn, depending on presence of binocular vision in a particular gaze

- diplopia or double vision - more seen in adults (maturity / plasticity of neural pathways) and suppression mechanisms of the brain in sorting out the images from the two eyes.

- cyclotropia, a cyclotorsional deviation of the eyes (rotation around the visual axis), particularly when the root cause is an oblique muscle paresis causing the hypertropia.

Treatment is usually unnecessary. In severe cases, surgery with a bilateral levator excision and frontalis brow suspension may be used.

Although treatment may be unnecessary, there may be social implications, especially in young children when venturing from a supportive home environment to a public environment (e.g., starting school). Continued support, including monitoring behavior and educating the child about his or her appearance as seen by others, is encouraged. Gradual or sudden withdrawal from interaction with others is a sign that may or may not be related to such behavior. Studies are being conducted to elucidate these implications.

The treatment of individuals with TCS may involve the intervention of professionals from multiple disciplines. The primary concerns are breathing and feeding, as a consequence of the hypoplasia of the mandibula and the obstruction of the hypopharynx by the tongue. Sometimes, they may require a tracheostomy to maintain an adequate airway, and a gastrostomy to assure an adequate caloric intake while protecting the airway. Corrective surgery of the face is performed at defined ages, depending on the developmental state.

An overview of the present guidelines:

- If a cleft palate is present, the repair normally takes place at 9–12 months old. Before surgery, a polysomnography with a palatal plate in place is needed. This may predict the postoperative situation and gives insight on the chance of the presence of sleep apnea (OSAS) after the operation.

- Hearing loss is treated by bone conduction amplification, speech therapy, and educational intervention to avoid language/speech problems. The bone-anchored hearing aid is an alternative for individuals with ear anomalies

- Zygomatic and orbital reconstruction is performed when the cranio-orbitozygomatic bone is completely developed, usually at the age of 5–7 years. In children, an autologous bone graft is mostly used. In combination with this transplantation, lipofilling can be used in the periorbital area to get an optimal result of the reconstruction. Reconstruction of the lower eyelid coloboma includes the use of a myocutaneous flap, which is elevated and in this manner closes the eyelid defect.

- External ear reconstruction is usually done when the individual is at least eight years old. Sometimes, the external auditory canal or middle ear can also be treated.

- The optimal age for the maxillomandibular reconstruction is controversial; as of 2004, this classification has been used:

1. Type I (mild) and Type IIa (moderate) 13–16 years

2. Type IIb (moderate to severe malformation) at skeletal maturity

3. Type III (severe) 6–10 years

- When the teeth are cutting, the teeth should be under supervision of an orthodontist to make sure no abnormalities occur. If abnormalities like dislocation or an overgrowth of teeth are seen, appropriate action can be undertaken as soon as possible.

- Orthognatic treatments usually take place after the age of 16 years; at this point, all teeth are in place and the jaw and dentures are mature. Whenever OSAS is detected, the level of obstruction is determined through endoscopy of the upper airways. Mandibular advancement can be an effective way to improve both breathing and æsthetics, while a chinplasty only restores the profile.

- If a nose reconstruction is necessary, it is usually performed after the orthognatic surgery and after the age of 18 years.

- The contour of the facial soft tissues generally requires correction at a later age, because of the facial skeletal maturity. The use of microsurgical methods, like the free flap transfer, has improved the correction of facial soft tissue contours. Another technique to improve the facial soft tissue contours is lipofilling. For instance, lipofilling is used to reconstruct the eyelids.

The disorder can be associated with a number of psychological symptoms, anxiety, depression, social phobia, body image disorders, and patients may be subjected to discrimination, bullying and name calling especially when young. A multi-disciplinary team and parental support should include these issues.