Treatments of NTDs depends on the severity of the complication. No treatment is available for anencephaly and infants usually do not survive more than a few hours. Aggressive surgical management has improved survival and the functions of infants with spina bifida, meningoceles and mild myelomeningoceles. The success of surgery often depends on the amount of brain tissue involved in the encephalocele. The goal of treatment for NTDs is to allow the individual to achieve the highest level of function and independence. Fetal surgery in utero before 26 weeks gestation has been performed with some hope that there is benefit to the final outcome including a reduction in Arnold–Chiari malformation and thereby decreases the need for a ventriculoperitoneal shunt but the procedure is very high risk for both mother and baby and is considered extremely invasive with questions that the positive outcomes may be due to ascertainment bias and not true benefit. Further, this surgery is not a cure for all problems associated with a neural tube defect. Other areas of research include tissue engineering and stem cell therapy but this research has not been used in humans.

Standard treatment is after delivery. There is tentative evidence about treatment for severe disease before delivery while the baby is inside the womb. As of 2014 the evidence; however, remains insufficient to determine benefits and harms.

Treatment of spina bifida during pregnancy is not without risk. To the mother, this includes scarring of the uterus. To the baby, there is the risk of preterm birth.

Broadly, there are two forms of prenatal treatment. The first is open fetal surgery, where the uterus is opened and the spina bifida repair performed. The second is via fetoscopy. These techniques may be an option to standard therapy.

Most individuals with myelomeningocele will need periodic evaluations by a variety of specialists:

- Physiatrists coordinate the rehabilitation efforts of different therapists and prescribe specific therapies, adaptive equipment, or medications to encourage as high of a functional performance within the community as possible.

- Orthopedists monitor growth and development of bones, muscles, and joints.

- Neurosurgeons perform surgeries at birth and manage complications associated with tethered cord and hydrocephalus.

- Neurologists treat and evaluate nervous system issues, such as seizure disorders.

- Urologists to address kidney, bladder, and bowel dysfunction – many will need to manage their urinary systems with a program of catheterization. Bowel management programs aimed at improving elimination are also designed.

- Ophthalmologists evaluate and treat complications of the eyes.

- Orthotists design and customize various types of assistive technology, including braces, crutches, walkers, and wheelchairs to aid in mobility. As a general rule, the higher the level of the spina bifida defect, the more severe the paralysis, but paralysis does not always occur. Thus, those with low levels may need only short leg braces, whereas those with higher levels do best with a wheelchair, and some may be able to walk unaided.

- Physical therapists, occupational therapists, psychologists, and speech/language pathologists aid in rehabilitative therapies and increase independent living skills.

Currently, the only effective treatment for encephaloceles is reparative surgery, generally performed during infancy. The extent to which it can be corrected depends on the location and size of the encephaloceles; however, large protrusions can be removed without causing major disability. Surgery repositions the bulging area back into the skull, removes the protrusions, and corrects the deformities, typically relieving pressure that can delay normal brain development. Occasionally, shunts are placed to drain excess cerebrospinal fluid from the brain.

The goals of treatment include:

- closure of open skin defects to prevent infection and desiccation of brain tissue

- removal of nonfunctional extracranial cerebral tissue with water-tight closure of the dura

- total craniofacial reconstruction with particular emphasis on avoiding the long-nose deformity (nasal elongation that results from depression of the cribiform plate and nasal placode). Without proper management, the long-nose deformity can be more obvious after repair.

Treatment for individuals with Dandy–Walker Syndrome generally consists of treating the associated problems, if needed.

A special tube (shunt) to reduce intracranial pressure may be placed inside the skull to control swelling. Endoscopic third ventriculostomy is also an option.

Treatment may also consist of various therapies such as occupational therapy, physiotherapy, speech therapy or specialized education. Services of a teacher of students with blindness/visual impairment may be helpful if the eyes are affected.

In 1996, the United States Food and Drug Administration published regulations requiring the addition of folic acid to enriched breads, cereals, flour and other grain products. It is important to note that during the first four weeks of pregnancy (when most women do not even realize that they are pregnant), adequate folate intake is essential for proper operation of the neurulation process. Therefore, women who could become pregnant are advised to eat foods fortified with folic acid or take supplements in addition to eating folate-rich foods to reduce the risks of serious birth defects.

In Canada, mandatory fortification of selected foods with folic acid has been shown to reduce the incidence of neural tube defects by 46%.

Women who may become pregnant are advised to get 400 micrograms of folic acid daily. Women who have previously given birth to a child with a neural tube defect may benefit from a supplement containing 4.0 mg/5.0 mg in the UK mg daily, following advice provided by their doctor.

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.

It is recommended that women who may become pregnant take 400 micrograms of folic acid daily.

Treatment for Klippel–Feil syndrome is symptomatic and may include surgery to relieve cervical or craniocervical instability and constriction of the spinal cord, and to correct scoliosis.

Failing non-surgical therapies, spinal surgery may provide relief. Adjacent segment disease and scoliosis are two examples of common symptoms associated with Klippel–Feil syndrome, and they may be treated surgically. The three categories treated for types of spinal cord deficiencies are massive fusion of the cervical spine (Type I), the fusion of 1 or 2 vertebrae (Type II), and the presence of thoracic and lumbar spine anomalies in association with type I or type II Klippel–Feil syndrome (Type III).

Adjacent segment disease can be addressed by performing cervical disc arthroplasty using a device such as the Bryan cervical disc prosthesis.

The option of the surgery is to maintain range of motion and attenuate the rate of adjacent segment disease advancement without fusion.

Another type of arthroplasty that is becoming an alternate choice to spinal fusion is Total Disc Replacement. Total disc replacement objective is to reduce pain or eradicate it.

Spinal fusion is commonly used to correct spinal deformities such as scoliosis. Arthrodesis is the last resort in pain relieving procedures, usually when arthroplasties fail.

The principal treatment of chordee is surgery in infancy, usually by a pediatric urologist. With chordees caused by circumcision, the preferred method of surgical treatment is a z-plasty. The preferred time for surgery is between the ages of 6 and 18 months and correction is usually successful.

While there is no current cure, the treatments for Chiari malformation are surgery and management of symptoms, based on the occurrence of clinical symptoms rather than the radiological findings. The presence of a syrinx is known to give specific signs and symptoms that vary from dysesthetic sensations to algothermal dissociation to spasticity and paresis. These are important indications that decompressive surgery is needed for patients with Chiari Malformation Type II. Type II patients have severe brain stem damage and rapidly diminishing neurological response.

Decompressive surgery involves removing the lamina of the first and sometimes the second or third cervical vertebrae and part of the occipital bone of the skull to relieve pressure. The flow of spinal fluid may be augmented by a shunt. Since this surgery usually involves the opening of the dura mater and the expansion of the space beneath, a dural graft is usually applied to cover the expanded posterior fossa.

A small number of neurological surgeons believe that detethering the spinal cord as an alternate approach relieves the compression of the brain against the skull opening (foramen magnum), obviating the need for decompression surgery and associated trauma. However, this approach is significantly less documented in the medical literature, with reports on only a handful of patients. It should be noted that the alternative spinal surgery is also not without risk.

Complications of decompression surgery can arise. They include bleeding, damage to structures in the brain and spinal canal, meningitis, CSF fistulas, occipito-cervical instability and pseudomeningeocele. Rare post-operative complications include hydrocephalus and brain stem compression by retroflexion of odontoid. Also, an extended CVD created by a wide opening and big duroplasty can cause a cerebellar "slump". This complication needs to be corrected by cranioplasty.

In certain cases, irreducible compression of the brainstem occurs from in front (anteriorly or ventral) resulting in a smaller posterior fossa and associated Chiari malformation. In these cases, an anterior decompression is required. The most commonly used approach is to operate through the mouth (transoral) to remove the bone compressing the brainstem, typically the odontoid. This results in decompressing the brainstem and therefore gives more room for the cerebellum, thus decompressing the Chiari malformation. Arnold Menzes, MD, is the neurosurgeon who pioneered this approach in the 1970s at the University of Iowa. Between 1984 and 2008 (the MR imaging era), 298 patients with irreducible ventral compression of the brainstem and Chiari type 1 malformation underwent a transoral approach for ventral cervicomedullary decompression at the University of Iowa. The results have been excellent resulting in improved brainstem function and resolution of the Chiari malformation in the majority of patients.

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

Hypospadias repair can be done in full-term, healthy infants at any time from 3 months of age. Premature babies generally have surgery done at 6 months or older. Using these guidelines, most babies can undergo repair as same-day surgery, without need to stay in the hospital afterwards.

The results of surgery are probably not influenced by the age at which repair is done, but older children are more likely to recall the event. Teens and adults typically spend one night in the hospital after surgery.

Surgery

Surgical intervention is warranted in patients who present with new onset neurological signs and symptoms or have a history of progressive neurological manifestations which can be related to this abnormality. The surgical procedure required for the effective treatment of diastematomyelia includes decompression (surgery) of neural elements and removal of bony spur. This may be accomplished with or without resection and repair of the duplicated dural sacs. Resection and repair of the duplicated dural sacs is preferred since the dural abnormality may partly contribute to the "tethering" process responsible for the symptoms of this condition.

Post-myelographic CT scanning provides individualized detailed maps that enable surgical treatment of cervical diastematomyelia, first performed in 1983.

Observation

Asymptomatic patients do not require surgical treatment. These patients should have regular neurological examinations since it is known that the condition can deteriorate. If any progression is identified, then a resection should be performed.

Because newborns can breathe only through their nose, the main goal of postnatal treatment is to establish a proper airway. Primary surgical treatment of FND can already be performed at the age of 6 months, but most surgeons wait for the children to reach the age of 6 to 8 years. This decision is made because then the neurocranium and orbits have developed to 90% of their eventual form. Furthermore, the dental placement in the jaw has been finalized around this age.

Hormones potentially increase the size of the penis, and have been used in children with proximal hypospadias who have a smaller penis. Numerous articles report testosterone injections or topical creams increase the length and circumference of the penis. However, few studies discuss the impact of this treatment on the success of corrective surgery, with conflicting results. Therefore, the role, if any, for preoperative hormone stimulation is not clear at this time.

Structural nasal deformities are corrected during or shortly after the facial bipartition surgery. In this procedure, bone grafts are used to reconstruct the nasal bridge. However, a second procedure is often needed after the development of the nose has been finalized (at the age of 14 years or even later).

Secondary rhinoplasty is based mainly on a nasal augmentation, since it has been proven better to add tissue to the nose than to remove tissue. This is caused by the minimal capacity of contraction of the nasal skin after surgery.

In rhinoplasty, the use of autografts (tissue from the same person as the surgery is performed on) is preferred. However, this is often made impossible by the relative damage done by previous surgery. In those cases, bone tissue from the skull or the ribs is used. However, this may give rise to serious complications such as fractures, resorption of the bone, or a flattened nasofacial angle.

To prevent these complications, an implant made out of alloplastic material could be considered. Implants take less surgery time, are limitlessly available and may have more favorable characteristics than autografts. However, possible risks are rejection, infection, migration of the implant, or unpredictable changes in the physical appearance in the long term.

At the age of skeletal maturity, orthognathic surgery may be needed because of the often hypoplastic maxilla. Skeletal maturity is usually reached around the age of 13 to 16. Orthognathic surgery engages in diagnosing and treating disorders of the face and teeth- and jaw position.

Around 5 years of age, surgical correction may be necessary to prevent any worsening of the deformity. If the mother has dysplasia, caesarian delivery may be necessary. Craniofacial surgery may be necessary to correct skull defects. Coxa vara is treated by corrective femoral osteotomies. If there is brachial plexus irritation with pain and numbness, excision of the clavicular fragments can be performed to decompress it. In case of open fontanelle, appropriate headgear may be advised by the orthopedist for protection from injury.

Surgery is not always recommended for syringomyelia patients. For many patients, the main treatment is analgesia. Physicians specializing in pain management can develop a medication and treatment plan to ameliorate pain. Medications to combat any neuropathic pain symptoms such as shooting and stabbing pains (e.g. gabapentin or pregabalin) would be first-line choices. Opiates are usually prescribed for pain for management of this condition. Facet injections are not indicated for treatment of syringomyelia.

Drugs have no curative value as a treatment for syringomyelia. Radiation is used rarely and is of little benefit except in the presence of a tumor. In these cases, it can halt the extension of a cavity and may help to alleviate pain.

In the absence of symptoms, syringomyelia is usually not treated. In addition, a physician may recommend not treating the condition in patients of advanced age or in cases where there is no progression of symptoms. Whether treated or not, many patients will be told to avoid activities that involve straining.

Since the natural history of syringomyelia is poorly understood, a conservative approach may be recommended. When surgery is not yet advised, patients should be carefully monitored. Periodic MRI's and physical evaluations should be scheduled at the recommendation of a qualified physician.

The heterogeneity of the Klippel–Feil syndrome has made it difficult to outline the diagnosis as well as the prognosis classes for this disease. Because of this, it has complicated the exact explanation of the genetic cause of the syndrome.

The prognosis for most individuals with KFS is good if the disorder is treated early on and appropriately. Activities that can injure the neck should be avoided, as it may contribute to further damage. Other diseases associated with the syndrome can be fatal if not treated, or if found too late to be treatable.

Most fetuses with triploidy do not survive to birth, and those that do usually pass within days. As there is no treatment for Triploidy, palliative care is given if a baby survives to birth. If Triploidy is diagnosed during the pregnancy, termination is often offered as an option due to the additional health risks for the mother (preeclampsia, a life-threatening condition, or choriocarcinoma, a type of cancer). Should a mother decide to carry until term or until a spontaneous miscarriage occurs, doctors will monitor her closely in case either condition develops.

Mosaic triploidy has an improved prognosis, but affected individuals have moderate to severe cognitive disabilities.

The first step after diagnosis is finding a neurosurgeon who is experienced in the treatment of syringomyelia. Surgery is the treatment for syringomyelia. Evaluation of the condition is necessary because syringomyelia can remain stationary for long periods of time, and in some cases progress rapidly.

Surgery of the spinal cord has certain characteristic risks associated with it, and the benefits of a surgical procedure on the spine have to be weighed against the possible complications associated with any procedure. Surgical treatment is aimed at correcting the condition that allowed the syrinx to form. It is vital to bear in mind that the drainage of a syrinx does not necessarily mean the elimination of the syrinx-related symptoms but rather is aimed at stopping progression. In cases involving an Arnold-Chiari malformation, the main goal of surgery is to provide more space for the cerebellum at the base of the skull and upper cervical spine without entering the brain or spinal cord. This often results in flattening or disappearance of the primary syrinx or cavity, over time, as the normal flow of cerebrospinal fluid is restored. If a tumor is causing syringomyelia, removal of the tumor is the treatment of choice, if this is considered to be safe.

Surgery results in stabilization or modest improvement in symptoms for most patients. Delay in treatment may result in irreversible spinal cord injury. Recurrence of syringomyelia after surgery may make additional operations necessary; these may not be completely successful over the long term.

In some patients it may also be necessary to drain the syrinx, which can be accomplished using a catheter, drainage tubes, and valves. This system is also known as a shunt. Shunts are used in both the communicating and noncommunicating forms of the disorder. First, the surgeon must locate the syrinx. Then, the shunt is placed into it with the other end draining cerebrospinal fluid (CSF) into a cavity, usually the abdomen. This type of shunt is called a ventriculoperitoneal shunt and is particularly useful in cases involving hydrocephalus. By draining syrinx fluid, a shunt can arrest the progression of symptoms and relieve pain, headache, and tightness. Syringomyelia shunts are not always successful and can become blocked as with other central nervous system shunts.

The decision to use a shunt requires extensive discussion between doctor and patient, as this procedure carries with it greater risk of injury to the spinal cord, infection, blockage, or hemorrhage and may not necessarily work for all patients. Draining the syrinx more quickly does not produce better outcomes, but a shunt may be required if the fluid in the syrinx is otherwise unable to drain.

In the case of trauma-related syringomyelia, the surgeon operates at the level of the initial injury. The syrinx collapses at surgery, but a tube or shunt is usually necessary to prevent re-expansion.

Although there is no cure for 13q deletion syndrome, symptoms can be managed, usually with the involvement of a neurologist, rehabilitation physician, occupational therapist, physiotherapist, psychotherapist, nutritionist, special education professional, and/or speech therapist. If the affected child's growth is particularly slow, growth hormone treatment can be used to augment growth. Plastic surgeries can repair cleft palates, and surgical repair or monitoring by a pediatric cardiologist can manage cardiac defects. Some skeletal, neurological, genitourinary, gastrointestinal, and ophthalmic abnormalities can be definitively treated with surgery. Endocrine abnormalities can often be managed medically. Special educators, speech and occupational therapists, and physiotherapists can help a child develop skills in and out of school.

Several studies have reported that life expectancy appears to be normal for people with CCD.

There is no cure or standard treatment for anencephaly and the prognosis for patients is death. Most anencephalic fetuses do not survive birth, accounting for 55% of non-aborted cases. Infants that are not stillborn will usually die within a few hours or days after birth from cardiorespiratory arrest.

Four recorded cases of anencephalic children surviving for longer periods of time are Stephanie Keene (better known as Baby K) of Falls Church, Virginia, USA, who lived for 2 years 174 days; Vitoria de Cristo, born in Brazil in January 2010 and surviving until July 17, 2012; Nickolas Coke of Pueblo, Colorado, USA, who lived for 3 years and 11 months, and died October 31, 2012; and Angela Morales, from Providence, Rhode Island, who live for 3 years and 9 months, and died December 16 2017.

In almost all cases, anencephalic infants are not aggressively resuscitated because there is no chance of the infant's ever achieving a conscious existence. Instead, the usual clinical practice is to offer hydration, nutrition, and comfort measures and to "let nature take its course". Artificial ventilation, surgery (to fix any co-existing congenital defects), and drug therapy (such as antibiotics) are usually regarded as futile efforts. Some clinicians and medical ethicists view even the provision of nutrition and hydration as medically futile.