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.

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.

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.

If only small amounts of torsion are present, cyclotropia may be without symptoms entirely and may not need correction, as the visual system can compensate small degrees of torsion and still achieve binocular vision ("see also:" cyclodisparity, cyclovergence). The compensation can be a motor response (visually evoked cyclovergence) or can take place during signal processing in the brain. In patients with cyclotropia of vascular origin, the condition often improves spontaneously.

Cyclotropia cannot be corrected with prism spectacles in the way other eye position disorders are corrected. (Nonetheless two Dove prisms can be employed to rotate the visual field in experimental settings.)

For cyclodeviations above 5 degrees, surgery has normally been recommended. Depending on the symptoms, the surgical correction of cyclotropia may involve a correction of an associated vertical deviation (hyper- or hypotropia), or a Harada–Ito procedure or another procedure to rotate the eye inwards, or yet another procedure to rotate it outwards. A cyclodeviation may thus be corrected at the same time with a correction of a vertical deviation (hyper- or hypotropia); cyclodeviations without any vertical deviation can be difficult to manage surgically, as the correction of the cyclodeviation may introduce a vertical deviation.

Cyclotropia is a form of strabismus in which, compared to the correct positioning of the eyes, there is a of one eye (or both) about the eye's visual axis. Consequently, the visual fields of the two eyes appear tilted relative to each other. The corresponding "latent" condition – a condition in which torsion occurs only in the absence of appropriate visual stimuli – is called cyclophoria.

Cyclotropia is often associated with other disorders of strabism, can result in double vision, and can cause other symptoms, in particular head tilt.

In some cases, subjective and objective cyclodeviation may result from surgery for oblique muscle disorders; if the visual system cannot compensate for it, cyclotropia and rotational double vision (cyclodiplopia) may result. The role of cyclotropia in vision disorders is not always correctly identified. In several cases of double vision, once the underlying cyclotropia was identified, the condition was solved by surgical cyclotropia correction.

Conversely, artificially causing cyclotropia in cats leads to reduced vision acuity, resulting in a defect similar to strabismic amblyopia.

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.