A placebo-controlled trial of plasmapheresis and IVIG for PANDAS was conducted at the NIH in the late 1990’s, with children randomly assigned (by the NIH pharmacy) to receive plasmapheresis (unblinded) or IVIG/sham IVIG (double blinded). At one month evaluations, placebo infusions produced no improvements in OC or tic symptoms, while 100% of the children receiving IVIG or plasmapheresis improved. The average improvement in OC symptoms was 45% for the group receiving IVIG and nearly 65% for the children receiving plasmapheresis. The results of the trial were sufficiently robust to cause the American Society of Apheresis to include plasmapheresis as a treatment option for PANDAS, as well as for Sydenham chorea.

For treatment guidelines, refer to the PANDAS Physicians Network. PPN’s goal is to help medical professionals understand, diagnose and treat PANS and PANDAS. The network provides research, diagnostic, and treatment tools. PPN Guidelines for Diagnostics and Therapeutics are developed by PPN committees and advisors from the top academic medical institutions in the United States. The members have worked with, treated, and studied the patients and the disorder. PANS and PANDAS are interdisciplinary disorders, so the relevant disciplines are represented on the PPN committees and special advisory council. Some of the disciplines include: Psychiatrists, Pediatric Neurologists, Immunologists, Microbiologists, Rheumatologists, Geneticists, Otolaryngologists, etc.

Currently treatment is only symptomatic and palliative. Treatment for manifestations, such as seizures, dystonia, sleep disorders, depression and anxiety, can be effectively managed. Physical and occupational therapy is recommended to help patients retain fine motor function for as long as possible Recent progress has been made in the application of enzyme-replacement, gene, and stem cell therapies for patients.

The treatment to battle the disease chorea-acanthocytosis is completely symptomatic. For example, Botulinum toxin injections can help to control orolingual dystonia.

Deep Brain Stimulation is a treatment that has varied effects on the people suffering from the symptoms of this disease, for some it has helped in a large way and for other people it did not help whatsoever, it is more effective on specific symptoms of the disease. Patients with chorea-acanthocytosis should undergo a cardiac evaluation every 5 years to look for cardiomyopathy.

There is currently no cure for SCA 6; however, there are supportive treatments that may be useful in managing symptoms.

Research suggests that paraphrenics respond well to antipsychotic drug therapy if doctors can successfully achieve sufficient compliance. Herbert found that Stelazine combined with Disipal was an effective treatment. It promoted the discharging of patients and kept discharged patients from being readmitted later. While behavior therapy may help patients reduce their preoccupation with delusions, psychotherapy is not currently of primary value.

Due to neuroferritinopathy’s genetic etiology, the disorder is not currently curable. Furthermore, progression of the disorder is unable to be effectively halted. Therefore current treatment focuses on managing symptoms of the disorder.

No medication is available to treat all symptoms. Botox has been shown to help with focal dystonia. The dopamine depleter Tetrabenazine shown to help with involuntary movements. Symptoms affecting movement (dystonia) have also been treated with L-Dopa, orphenadrine, benzhexol, sulpiride, diazepam, clonazepam, and deanol. Parkinsonian symptoms were not decreased by L-Dopa. Iron supplements should be avoided.

Loss of language and skills related to social interaction and self-care are serious. The affected children face ongoing disabilities in certain areas and require long term care. Treatment of CDD involves both behavior therapy, environmental therapy and medications.

- Behavior therapy: The main aim of Applied Behavior Analysis (ABA) is to systematically teach the child to relearn language, self-care and social skills. The treatment programs designed in this respect "use a system of rewards to reinforce desirable behaviors and discourage problem behavior." ABA programs may be designed by a board-certified specialist in behavior analysis called a "BCBA" (Board Certified Behavior Analyst), but ABA is also widely used by a number of other health care personnel from different fields like psychologists, speech therapists, physical therapists and occupational therapists with differing levels of expertise. Parents, teachers and caregivers are instructed to use these behavior therapy methods at all times.

- Environmental Therapy: Sensory Enrichment Therapy uses enrichment of the sensory experience to improve symptoms in autism, many of which are common to CDD.

- Medications: There are no medications available to directly treat CDD. Antipsychotic medications are used to treat severe behavior problems like aggressive stance and repetitive behavior patterns. Anticonvulsant medications are used to control seizures.

One treatment methodogy that is very promising for the treatment of camptocormia is deep brain stimulation. Previously, deep brain stimulation and bilateral stimulation of the subthalamic nucleus and/or globus pallidus internus have been used to treat patients with Parkinson's disease. Studies have shown that similar treatments could be used on patients with severe camptocormia. By using the Burke-Fahn-Marsden Dystonia Rating Scale before and after treatment, it was found that patients experienced significant functional improvement in the ability to walk.

Treatment is palliative, not curative (as of 2009).

Treatment options for lower limb weakness such as foot drop can be through the use of Ankle Foot Orthoses (AFOs) which can be designed or selected by an Orthotist based upon clinical need of the individual. Sometimes tuning of rigid AFOs can enhance knee stability.

Cardiac and respiratory complications are treated symptomatically. Physical and occupational therapy may be beneficial for some patients. Alterations in diet may provide temporary improvement but will not alter the course of the disease. Genetic counseling can provide families with information regarding risk in future pregnancies.

On April 28, 2006 the US Food and Drug Administration approved a Biologic License Application (BLA) for Myozyme (alglucosidase alfa, rhGAA), the first treatment for patients with Pompe disease, developed by a team of Duke University researchers. This was based on enzyme replacement therapy using biologically active recombinant human alglucosidase alfa produced in Chinese Hamster Ovary cells. Myozyme falls under the FDA Orphan Drug designation and was approved under a priority review.

The FDA has approved Myozyme for administration by intravenous infusion of the solution. The safety and efficacy of Myozyme were assessed in two separate clinical trials in 39 infantile-onset patients with Pompe disease ranging in age from 1 month to 3.5 years at the time of the first infusion. Myozyme treatment clearly prolongs ventilator-free survival and overall survival. Early diagnosis and early treatment leads to much better outcomes. The treatment is not without side effects which include fever, flushing, skin rash, increased heart rate and even shock; these conditions, however, are usually manageable.

Myozyme costs an average of US$300,000 a year and must be taken for the patients' entire life, so some American insurers have refused to pay for it. On August 14, 2006, Health Canada approved Myozyme for the treatment of Pompe disease. On June 14, 2007 the Canadian Common Drug Review issued their recommendations regarding public funding for Myozyme therapy. Their recommendation was to provide funding to treat a very small subset of Pompe patients (Infants less one year of age with cardiomyopathy). Genzyme received broad approval in the European Union. On May 26, 2010 FDA approved Lumizyme, a similar version of Myozyme, for the treament of late-onset Pompe disease.

A new treatment option for this disease is called Lumizyme. Lumizyme and Myozyme have the same generic ingredient (Alglucosidase Alfa) and manufacturer (Genzyme Corporation). The difference between these two products is in the manufacturing process. Today, the Myozyme is made using a 160-L bioreactor, while the Lumizyme uses a 4000-L bioreactor. Because of the difference in the manufacturing process, the FDA claims that the two products are biologically different. Moreover, Lumizyme is FDA approved as replacement therapy for late-onset (noninfantile) Pompe disease without evidence of cardiac hypertrophy in patients 8 years and older. Myozyme is FDA approved for replacement therapy for infantile-onset Pompe disease.

Recent studies on chaperone molecules to be used with myozyme are starting to show promising results on animal models.

On April 27, 2017, the U.S. Food and Drug Administration approved Brineura (cerliponase alfa) as the first specific treatment for NCL. Brineura is enzyme replacement therapy manufactured through recombinant DNA technology. The active ingredient in Brineura, cerliponase alpha, is intended to slow loss of walking ability in symptomatic pediatric patients 3 years of age and older with late infantile neuronal ceroid lipofuscinosis type 2 (CLN2), also known as tripeptidyl peptidase-1 (TPP1) deficiency. Brineura is administered into the cerebrospinal fluid by infusion via a surgically implanted reservoir and catheter in the head (intraventricular access device).

A painkiller available in several European countries, Flupirtine, has been suggested to possibly slow down the progress of NCL, particularly in the juvenile and late infantile forms. No trial has been officially supported in this venue, however. Currently the drug is available to NCL families either from Germany, Duke University Medical Center in Durham, North Carolina, and the Hospital for Sick Children in Toronto, Ontario.

There is no known cure for Niemann–Pick type C, nor is there any FDA-standard approved disease modifying treatment. Supportive care is essential and substantially improves the quality of life of people affected by NPC. The therapeutic team may include specialists in neurology, pulmonology, gastroenterology, psychiatrist, orthopedics, nutrition, physical therapy and occupational therapy. Standard medications used to treat symptoms can be used in NPC patients. As patients develop difficulty with swallowing, food may need to be softened or thickened, and eventually, parents will need to consider placement of a gastrostomy tube (g-tube, feeding tube).

An observational study is underway at the National Institutes of Health to better characterize the natural history of NPC and to attempt to identify markers of disease progression.

Although there is no known cure for Krabbe disease, bone marrow transplantation has been shown to benefit cases early in the course of the disease. Generally, treatment for the disorder is symptomatic and supportive. Physical therapy may help maintain or increase muscle tone and circulation. Cord blood transplants have been successful in stopping the disease as long as they are given before overt symptoms appear.

Metabolic disorders can be treatable by nutrition management, especially if detected early. It is important for dieticians to have knowledge of the genotype to therefore create a treatment that will be more effective for the individual.

In 2014 the European Medicines Agency (EMA) granted orphan drug designation to arimoclomol for the treatment of Niemann-Pick type C. This was followed in 2015 by the U.S. Food & Drug Administration (FDA). Dosing in a placebo-controlled phase II/III clinical trial to investigate treatment for Niemann-Pick type C (for patients with both type C1 and C2) using arimoclomol began in 2016. Arimoclomol, which is orally administered, induces the heat shock response in cells and is well tolerated in humans.

Because lack of sialic acid appears to be part of the pathology of IBM caused by GNE mutations, clinical trials with sialic acid supplements, and with a precursor of sialic acid, N-Acetylmannosamine, have been conducted, and as of 2016 further trials were planned.

There is no cure for congenital alpha-mannosidosis. Treatment is limited to reducing or controlling the symptoms of this disorder by, for example, taking medication to control seizures, using a hearing aid to assist with hearing loss, and by having routine physical therapy to assist with muscular pain and weakness. In some cases, a wheelchair is recommended if muscle or spinal impairments immobilize the individual affected. Despite early reports to the contrary, bone marrow transplants performed at an early age have shown promise in halting the progression of this disorder.

Due to the wide range of causes of camptocormia, there is no one treatment that suits all patients. In addition, there is no specific pharmacological treatment for primary BSS. The use of analgesic drugs depends entirely on the intensity of the back pain. Muscular-origin BSS can be alleviated by positive lifestyle changes, including physical activity, walking with a cane, a nutritious diet, and weight loss. Worsening of symptoms is possible but rare in occurrence.

Treatment of the underlying cause of the disease can alleviate the condition in some individuals with secondary BSS. Other treatment options include drugs, injections of botulinum toxin, electroconvulsive therapy, deep brain stimulation, and surgical correction. Unfortunately, many of the elderly individuals affected by the BSS are not treated surgically due to age-related physical ailments and the long postoperative recovery period.

Current methods in treating early-onset schizophrenia follow a similar approach to the treatment of adult schizophrenia. Although modes of treatment in this population is largely understudied, the use of antipsychotic medication is commonly the first line of treatment in addressing symptoms. Recent literature has failed to determine if typical or atypical antipsychotics are most effective in reducing symptoms and improving outcomes. When weighing treatment options, it is necessary to consider the adverse effects of various medications used to treat schizophrenia and the potential implications of these effects on development. A 2013 systematic review compared the efficacy of atypical antipsychotics versus typical antipsychotics for adolescents:

Madaan et al. wrote that studies report efficacy of typical neuroleptics such as thioridazine, thiothixene, loxapine and haloperidol, high incidence of side effects such as extrapyramidal symptoms, akathisia, dystonias, sedation, elevated prolactin, tardive dyskinesia.

Currently Sandhoff disease does not have any standard treatment and does not have a cure. However, a person suffering from the disease needs proper nutrition, hydration, and maintenance of clear airways. To reduce some symptoms that may occur with Sandhoff disease, the patient may take anticonvulsants to manage seizures or medications to treat respiratory infections, and consume a precise diet consisting of puree foods due to difficulties swallowing. Infants with the disease usually die by the age of 3 due to respiratory infections. The patient must be under constant surveillance because they can suffer from aspiration or lack the ability to change from the passageway to their lungs versus their stomach and their spit travels to the lungs causing bronchopneumonia. The patient also lacks the ability to cough and therefore must undergo a treatment to shake up their body to remove the mucus from the lining of their lungs. Medication is also given to patients to lessen their symptoms including seizures.

Currently the government is testing several treatments including N-butyl-deoxynojirimycin in mice, as well as stem cell treatment in humans and other medical treatments recruiting test patients.

There is no known "cure" for PDD-NOS, but there are interventions that can have a positive influence. Early and intensive implementation of evidence-based practices and interventions are generally believed to improve outcomes. Most of these are individualized special education strategies rather than medical or pharmaceutical treatment; the best outcomes are achieved when a team approach among supporting individuals is utilized.

Some of the more common therapies and services include:

- Visual and environmental supports, visual schedules

- Applied behavior analysis

- Discrete trial instruction (part of applied behavior analysis)

- Social stories and comic strip conversations

- Physical and occupational therapy

Pharmacotherapy for acute episodes of depression usually is effective and free of complications. Underuse or misuse of antidepressants and prescribing inadequate dosages are the most common mistakes physicians make when treating elderly patients for depression. Only 10 to 40 percent of depressed elderly patients are given medication. Antidepressants, in general, may also work by playing a neuroprotective role in how they relieve anxiety and depression. It's thought that antidepressants may increase the effects of brain receptors that help nerve cells keep sensitivity to glutamate which is an organic compound of a nonessential amino acid. This increased support of nerve cells lowers glutamate sensitivity, providing protection against the glutamate overwhelming and exciting key brain areas related to depression. Antidepressant medications are often the first treatment choice for adults with moderate or severe depression, sometimes along with psychotherapy. Although antidepressants may not cure depression, they can lead to remission, which is the disappearance or nearly complete reduction of depression symptoms.

Response to treatment is variable and the long-term and functional outcome is unknown. To provide a basis for improving the understanding of the epidemiology, genotype/phenotype correlation and outcome of these diseases their impact on the quality of life of patients, and for evaluating diagnostic and therapeutic strategies a patient registry was established by the noncommercial International Working Group on Neurotransmitter Related Disorders (iNTD).