There is no standard course of treatment for cerebellar hypoplasia. Treatment depends upon the underlying disorder and the severity of symptoms. Generally, treatment is symptomatic and supportive. Balance rehabilitation techniques may benefit those experiencing difficulty with balance. Treatment is based on the underlying disorder and the symptom severity. Therapies include physical, occuptational, speech/language, visual, psych/ behavioral meds, special education.

The prognosis of this developmental disorder is highly based on the underlying disorder. Cerebellar hypoplasia may be progressive or static in nature. Some cerebellar hypoplasia resulting from congenital brain abnormalities/malformations are not progressive. Progressive cerebellar hypoplasia is known for having poor prognosis, but in cases where this disorder is static, prognosis is better.

An endoscopic third ventriculostomy (ETV) is a procedure where an incision is made in the bottom of the third ventricle to make a drainage point for CSF to flow out of. The procedure is minimally invasive and is performed endoscopically. The goal in the surgery is to create a path for communication between the third ventricle and the subarachnoid space outside the brain for reabsorption of CSF. ETV has a higher failure rate than shunting during the first 3 postoperative months, but after this time the risk of failure progressively drops to become half as high as the failure risk for shunting.

This treatment does not place a foreign body into the patient so there is a much lower risk of infection as compared to a shunt procedure. Along with not implanting a device, this procedure avoids mechanical issues like disconnection, over or underdrainage, and valve dysfunction. The surgery begins by entering the right or left lateral ventricle endoscopically through a burr hole. The third ventricle is identified and entered as well, and an incision is made in the floor of the ventricle and enlarged as necessary with tools such as forceps or Fogarty catheters. If a membrane prevents CSF flow between the ventricle and the subarachnoid space, then an incision is made in the membrane as well. Ideally this procedure can be performed near the midline of the brain with minimal side-to-side motions of the endoscope so as to not tear tissues and cause further complications.

Research has found that this procedure has a 75% success rate, that 72% of ETV surgeries are still correctly functioning after 15 years, and that patients have shorter hospital stays recovering as compared to shunting. If the procedure does not successfully cure the aqueductal stenosis, a second surgery can be performed to enlarge the incision or implant a shunt. Problems that can lead to these failures and require additional surgery include the stoma becoming closed or a new membrane forming across the stoma over time. Currently there is no universal decision about whether this should be performed in children, as infants have a higher tendency to have a membrane form over the incision which means that an additional surgery would have to be performed.

An extracranial shunt is essentially a sturdy tube with a catheter on one end to drain the third ventricle. The shunt also has a valve which serves to maintain one-way flow of the CSF and regulates the flow rate. The end with the catheter is placed in the third ventricle to drain the excess CSF and the other end is placed in the peritoneal cavity or atrium of the heart (making it a ventriculoperitoneal or ventriculoatrial shunt, respectively). The excess CSF which is diverted to a cavity is then reabsorbed by the surrounding tissue where it is drained to.

The procedure to insert this device is a technically straightforward endoscopic surgery with a low mortality rate (essentially 0% mortality since the 1970s). If the shunt has an adjustable valve the current method of setting the valve pressure is to choose one setting, observe the patient to see if CSF flow improves and the symptoms lessen over time, and adjust the pressure setting as needed if improvement isn't seen. For example, if there is not enough CSF flow, another surgery is performed to lower the valve pressure so that less force needs to be applied to open the valve and thereby drain more CSF.

This treatment method has several possible problems with it (with a 50% failure rate in 2 years), and unfortunately shunt malfunctions and associated complications cause a death rate of 1.2% per year. Problems which can necessitate a secondary surgery to fix them include: mechanical failure, incorrect catheter size, inappropriate valve drainage pressure, and infection.

- Inappropriate valve pressure can lead to "overdraining" or "underdraining", both of which should be treated by adjusting the valve pressure. Overdraining occurs when the valve pressure is too low and CSF flows out of the third ventricle too quickly. The ventricle then collapses and blood vessles can be torn in the process. This in turn can lead to headache, hemorrhage, or slit ventricle syndrome. Underdraining occurs when the valve pressure is too high and CSF flows out too slowly. This results in symptoms of hydrocephalus as the CSF is still collecting rather than being absorbed or diverted.

- Risk of infection is due to the fact that a foreign object is being introduced into the body. Infection can have symptoms of fever and soreness of the neck and shoulders.