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.

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.

The general purpose of the following treatment methods is to divert the flow of CSF from the blocked aqueduct, which is causing the buildup of CSF, and allow the flow to continue. Another goal of these treatments is to reduce the stress within the ventricles. Studies have not shown that either of the following treatments results in a higher IQ of the patient, and there is not statistical difference in a patient's quality of life based on treatment method. The following treatment methods are not used for aqueductal stenosis caused by tumor compression; if the obstruction is a direct result of tumor compression, CSF flow may be normalized by the surgical removal of the tumor.

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.