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 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.

While preventive measures, such as taking breaks from activities that cause eye strain are suggested, there are certain treatments which a person suffering from the condition can take to ease the pain or discomfort that the affliction causes. Perhaps the most effective of these is to remove all light sources from a room and allow the eyes to relax in darkness. Free of needing to focus, the eyes will naturally relax over time, and relieve the discomfort that comes with the strain. Cool compresses also help to some degree, though care should be taken to not use anything cold enough to damage the eyes themselves (such as ice). A number of companies have released "computer glasses" which, through the use of specially tinted lenses, help alleviate many of the factors which cause eye strain, though they do not completely prevent it. Rather, they just make it harder to strain the eye.

When the fusional vergence system can no longer hold back heterophoria, the phoria manifests. In this condition, the eyes deviate from the fixating position.

There are several methods to quantify fixation disparity. The Mallett card, the Bernell lantern slide, the Wesson Card and the Disparometer may be used. A patient's associated phoria is the amount of prism needed to reduce their fixation disparity to zero minutes of arc.

The Mallett Fixation Disparity Unit

Instrument used to measure the associated heterophoria (or compensating prism). It consists of a small central fixation letter X surrounded by two letters O, one on each side of X, the three letters being seen binocularly, and two coloured polarized vertical bars in line with the centre of the X which are seen by each eye separately. The instrument can be swung through 90° to measure any vertical fixation disparity. The associated phoria is indicated by the misalignment of the two polarized bars when the subject fixates the X through cross-polarized filters in front of the eyes. The amount of associated phoria is given by the value of the base-in or base-out prism power necessary to produce alignment and the eye. The unit can also be used to detect suppression. See Disparometer; associated heterophoria; uncompensated heterophoria.

In order to understand how heterophoria occurs, we must understand of how the eye can maintain proper fixation with non aligned visual axis. Heterophoria is actually the misalignment of the visual axis of both eyes. In other words, one or both eyes are not properly fixated to an object of interest. However, we must know that the eyes have a fusional vergence system which corrects this misalignment.

Fixation disparity exists when there is a small misalignment of the eyes when viewing with binocular vision. The misaligment may be vertical, horizontal or both. The misalignment (a few minutes of arc) is much smaller than that of strabismus, which prevents binocular vision, although it may reduce a patient's level of stereopsis. A patient may or may not have fixation disparity and a patient may have a different fixation disparity at distance than near.

Sometimes asthenopia can be due to specific visual problems—for example, uncorrected refraction errors or binocular vision problems such as accommodative insufficiency or heterophoria. It is often caused by the viewing of monitors such as those of computers or phones for prolonged periods of time.

Esophoria is an eye condition involving inward deviation of the eye, usually due to extra-ocular muscle imbalance. It is a type of heterophoria.

Causes include:

- Refractive errors

- Divergence insufficiency

- Convergence excess; this can be due to nerve, muscle, congenital or mechanical anomalies.

Unlike esotropia, fusion is possible and therefore diplopia is uncommon.

Exophoria can be caused by several factors, which include:

- Refractive errors - distance and near deviation approximately equal.

- Divergence excess - exodeviation is more than 15 dioptres greater for distance than near deviation.

- Convergence insufficiency - near exodeviation greater than distance deviation.

These can be due to nerve, muscle, or congenital problems, or due to mechanical anomalies. Unlike exotropia, fusion is possible in this condition, causing diplopia to be uncommon.

Exophoria is a form of heterophoria in which there is a tendency of the eyes to deviate outward. During examination, when the eyes are dissociated, the visual axes will appear to diverge away from one another.

The axis deviation in exophoria is usually mild compared with that of exotropia.