Symptoms may be treated by wearing wider shoes to relieve pressure, or patient can wear padding around the toes. Surgery is also an option, if the pain and discomfort cannot be treated, or for cosmetic reasons. In this procedure, the short metatarsal is typically cut and a piece of bone is grafted between the two ends. In some cases an external fixator may be attached to the metatarsal with pins. Within the external fixator is an adjustable screw that must be turned (per doctors' orders) to lengthen the gap between bone segments, so the bone will regrow to the appropriate shape.

Following surgery, crutches or a knee scooter should be used to keep all weight off the surgically repaired foot for 3 months. After this period, orthopedic shoes or boots may be used.

Asymptomatic anatomical variations in feet generally do not need treatment.

Conservative treatment for foot pain with Morton's toe may involve exercises or placing a flexible pad under the first toe and metatarsal; an early version of the latter treatment was once patented by Dudley Joy Morton. Restoring the Morton’s toe to normal function with proprioceptive orthotics can help alleviate numerous problems of the feet such as metatarsalgia, hammer toes, bunions, Morton's neuroma, plantar fasciitis, and general fatigue of the feet. Rare cases of disabling pain are sometimes treated surgically.

Brachymetatarsia or hypoplastic metatarsal is a condition in which there is one or more abnormally short or overlapping toes metatarsals. This condition may result due to a congenital defect or it may be an acquired condition. It most frequently involves the fourth metatarsal. If it involves the first metatarsal, the condition is known as Morton's syndrome. Treatment is via a number of differing surgical procedures.

The most common symptom experienced due to Morton's toe is callusing and/or discomfort of the ball of the foot at the base of the second toe. The first metatarsal head would normally bear the majority of a person's body weight during the propulsive phases of gait, but because the second metatarsal head is farthest forward, the force is transferred there. Pain may also be felt in the arch of the foot, at the ankleward end of the first and second metatarsals.

In shoe-wearing cultures, Morton's toe can be problematic. For instance, wearing shoes with a profile that does not accommodate a longer second toe may cause foot pain. A small (80-person) study found no statistically significant difference in the frequency of longer second toes between people with and without ingrown toenails, but tight and ill-fitting shoes are generally considered to increase the risk of ingrown toenails, and shoes are often too tight on the toes.