Patients must have early consultation with craniofacial and orthopaedic surgeons, when craniofacial, clubfoot, or hand correction is indicated to improve function or aesthetics. Operative measures should be pursued cautiously, with avoidance of radical measures and careful consideration of the abnormal muscle physiology in Freeman–Sheldon syndrome. Unfortunately, many surgical procedures have suboptimal outcomes, secondary to the myopathy of the syndrome.

When operative measures are to be undertaken, they should be planned for as early in life as is feasible, in consideration of the tendency for fragile health. Early interventions hold the possibility to minimise developmental delays and negate the necessity of relearning basic functions.

Due to the abnormal muscle physiology in Freeman–Sheldon syndrome, therapeutic measures may have unfavourable outcomes. Difficult endotracheal intubations and vein access complicate operative decisions in many DA2A patients, and malignant hyperthermia (MH) may affect individuals with FSS, as well. Cruickshanks et al. (1999) reports uneventful use of non-MH-triggering agents. Reports have been published about spina bifida occulta in anaesthesia management and cervical kyphoscoliosis in intubations.

Pregnant mothers are advised to take folic acid supplements to reduce risk of iniencephaly by up to 70%. Pregnant mothers are also advised not to take antiepileptic drugs, diuretics, antihistamines, and sulfa drugs, all of which have been associated with increased risk for neural tube defects.

Patients and their parents must receive psychotherapy, which should include marriage counselling. Mitigation of lasting psychological problems, including depression secondary to chronic illness and posttraumatic stress disorder (PTSD), can be very successfully addressed with early interventions. This care may come from the family physician, or other attending physician, whoever is more appropriate; specialist care is generally not required. Lewis and Vitulano (2003) note several studies suggesting predisposal for psychopathology in paediatric patients with chronic illness. Esch (2002) advocates preventive psychiatry supports to facilitate balance of positive and negative stressors associated with chronic physical pathology. Patients with FSS should have pre-emptive and ongoing mixed cognitive therapy-psychodynamic psychotherapy for patients with FSS and cognitive-behavioural therapy (CBT), if begun after onset of obvious pathology.

Adler (1995) cautioned the failure of modern medicine to implement the biopsychosocial model, which incorporates all aspects of a patient’s experience in a scientific approach into the clinical picture, often results in chronically-ill patients deferring to non-traditional and alternative forms of therapy, seeking to be understood as a whole, not a part, which may be problematic among patients with FSS.

Furthermore, neuropsychiatry, physiological, and imaging studies have shown PTSD and depression to be physical syndromes, in many respects, as they are psychiatric ones in demonstrating limbic system physiological and anatomy disturbances. Attendant PTSD hyperarousal symptoms, which additionally increase physiological stress, may play a part in leading to frequent MH-like hyperpyrexia and speculate on its influence on underlying myopathology of FSS in other ways. PTSD may also bring about developmental delays or developmental stagnation, especially in paediatric patients.

With psychodynamic psychotherapy, psychopharmacotherapy may need to be considered. Electroconvulsive therapy (ECT) is advised against, in light of abnormal myophysiology, with predisposal to MH.

Since newborns with iniencephaly so rarely survive past childbirth, a standard treatment does not exist.

Prognosis is poor. Previous research suggested a 100% mortality rate for those with acrania. This disease is rare, occurring in 1 in 20,000 live births.

In order to better manage an acrania diagnosis, early detection is of extreme importance so that actions may be taken to help the mother and child. Families may choose either to terminate the pregnancy, or to carry the child to term. Acrania may cause a fetus to spontaneously abort before reaching term.

Agnathia (also termed hypognathous) is absence of a portion or the entirety of one or both jaws. It is a very rare condition.

Otocephaly (from the Greek words "οτο", meaning “ear”, and "κεφάλη", meaning "head") is a type of head disorder (cephalic disorder).

This is a lethal condition in which the primary feature is the total or virtual absence of the lower jaw (a developmental anomaly called agnathia). The “oto” in the name refers to the relationship of the ears to the face in this disorder.

The condition is considered lethal because of a poorly functioning airway.

In otocephaly, agnathia may occur alone or together with holoprosencephaly.

Microstomia ("micro-" a combining form meaning small + "-stomia" a combining form meaning mouth = (abnormally) "small mouth") is a clinical feature of many craniofacial syndromes, including Freeman-Sheldon syndrome and Sheldon-Hall syndromes (or distal arthrogryposis multiplex congenita). It may present with whistling-face feature, as well, as in Freeman-Sheldon syndrome. In this syndrome, it impairs alimentation and may require repeated oral surgeries (called commissurotomy) to improve function.

It can also be a feature of systemic scleroderma.

Acrania is a rare congenital disorder that occurs in the human fetus in which the flat bones in the cranial vault are either completely or partially absent. The cerebral hemispheres develop completely but abnormally. The condition is frequently, though not always, associated with anencephaly. The fetus is said to suffer from acrania if it meets the following criteria: the fetus should have a perfectly normal facial bone, a normal cervical column but without the fetal skull and a volume of brain tissue equivalent to at least one third of the normal brain size.